# HG changeset patch
# User pjbriggs
# Date 1456323918 18000
# Node ID 0abe6bac47a68d2bc474aafc15f25c69b8b156ab
planemo upload for repository https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator commit 97d556dae96db5457590a3a257392b6e4093a912-dirty
diff -r 000000000000 -r 0abe6bac47a6 README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,145 @@
+RnaChipIntegrator: integrated analysis of gene expression and ChIP data
+=======================================================================
+
+Galaxy tool wrappers for running the RnaChipIntegrator program
+(http://fls-bioinformatics-core.github.com/RnaChipIntegrator/) for integrated
+analyses of gene expression and ChIP data.
+
+There are two tools available that are built around RnaChipIntegrator:
+
+- General RnaChipIntegrator tool that allows any peaks to be analysed against
+ any gene list
+- A "cannonical gene" variant which allows ChIP peaks to be analysed against a
+ list of cannonical genes for different genomes
+
+Automated installation
+======================
+
+Installation via the Galaxy Tool Shed will take of installing the tool wrapper
+and the RnaChipIntegrator programs, installing the .loc files, and setting the
+appropriate environment variables.
+
+Manual Installation
+===================
+
+There are three files to install:
+
+- ``rnachipintegrator_wrapper.xml`` (the Galaxy tool definition for general usage)
+- ``rnachipintegrator_canonical_genes.xml`` (tool definition for the "canonical
+ gene" variant)
+- ``rnachipintegrator_wrapper.sh`` (the shell script wrapper)
+
+The suggested location is in a ``tools/rnachipintegrator/`` folder. You will then
+need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
+by adding the lines:
+
+
+
+
+You will also need to install the RnaChipIntegrator program:
+
+- http://fls-bioinformatics-core.github.com/RnaChipIntegrator/
+
+In addition for the cannonical gene and histone modification variants, it's
+necessary to copy the .loc.sample files to .loc Galaxy's ``tool-data`` folder:
+
+- **Cannonical genes**: its necessary to manually acquire cannonical gene
+ list files from UCSC and then add appropriate references in the
+ ``rnachipintegrator_canonical_genes.loc`` file.
+
+If you want to run the functional tests, copy the sample test files under
+``test-data`` to Galaxy's ``test-data/`` directory. Then:
+
+ ./run_tests.sh -id fls_rnachipintegrator_wrapper
+
+
+How to get canonical gene data
+==============================
+
+Getting canonical gene info from UCSC is covered in the screencast at
+http://blog.openhelix.eu/?p=6097
+
+In summary:
+
+- **UCSC genome browser:** if multiple versions of each gene are visible (e.g.
+ if you view 'human Feb 2009 GRCh37/hg19' positions chr17:41,100,000-41,300,000)
+ then:
+
+ - Scroll down to the Gene & Gene Prediction section
+ - Click on the UCSC genes link
+ - Uncheck the tickbox next to splice variants and resubmit to view without
+ duplicates.
+
+- **UCSC table browser:** to obtain the canonical set of genes from the table
+ browser:
+
+ - Select knownCanonical from the table menu
+ - Select selected fields from primary & related tables from the output format menu
+ - Click on Get output
+ - Select the fields of interest (e.g. 'chrom', 'chromStart', 'chromEnd' from the
+ 'knownCanonical' table plus 'geneSymbol' from the kgXref table.)
+ - Click on Get output to get the data for download
+
+(Hint: to also get strand direction information i.e. +/-, also allow selection
+from the refGene table, and select the strand field.)
+
+
+Note on Excel output files and Galaxy
+=====================================
+
+RnaChipIntegrator produces an Excel spreadsheet as one of its outputs,
+however Galaxy is not currently set up by default to handle these.
+
+To enable Excel (XLS) output file handling in Galaxy, edit the
+``datatypes_conf.xml`` file and add:
+
+
+
+Restarting Galaxy should mean that the browser correctly handles Excel outputs
+from RnaChipIntegrator.
+
+History
+=======
+
+========== ======================================================================
+Version Changes
+---------- ----------------------------------------------------------------------
+1.0.0.0 - Update to use latest ``RnaChipIntegrator`` version 1.0.0.
+0.5.0-0 - Significant update to bring tools in line with
+ ``RnaChipIntegrator`` version 0.5.0, including removing the
+ distinction between 'regions' and 'summits' for input peaks,
+ and otherwise attempting to simplify the tools for users.
+0.4.4-0 - Initial version pushed to toolshed
+========== ======================================================================
+
+
+Developers
+==========
+
+This tool is developed on the following GitHub repository:
+https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/rnachipintegrator
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the ``package_rnachipintegrator_wrapper.sh`` script.
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff -r 000000000000 -r 0abe6bac47a6 data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,97 @@
+#!/usr/bin/env python
+#
+
+import sys
+import os
+import optparse
+import shutil
+
+from galaxy.util.json import from_json_string, to_json_string
+
+# Download file from specified URL and put into local subdir
+
+if __name__ == '__main__':
+ #Parse Command Line
+ parser = optparse.OptionParser()
+ options,args = parser.parse_args()
+ print "options: %s" % options
+ print "args : %s" % args
+ if len(args) != 2:
+ p.error("Need to supply JSON file name and description text")
+
+ # Read the JSON supplied from the data manager tool
+ # Results from this program will be returned via the
+ # same file
+ jsonfile = args[0]
+ params = from_json_string(open(jsonfile).read() )
+ print "%s" % params
+
+ # Extract the data from the input JSON
+ # See https://wiki.galaxyproject.org/Admin/Tools/DataManagers/HowTo/Define?highlight=%28\bAdmin%2FTools%2FDataManagers\b%29
+ # for example of JSON
+ #
+ # We want the values set in the data manager XML
+ dbkey = params['param_dict']['dbkey']
+ description = args[1].strip()
+ identifier = params['param_dict']['unique_id'].strip()
+ # Where to put the output file
+ # Nb we have to make this ourselves, it doesn't exist by default
+ target_dir = params['output_data'][0]['extra_files_path']
+ os.mkdir(target_dir)
+
+ method = params['param_dict']['reference_source']['reference_source_selector']
+
+ # Dictionary for returning to data manager
+ data_manager_dict = {}
+ data_manager_dict['data_tables'] = dict()
+
+ if method == 'server':
+ # Pull in a file from the server
+ filename = params['param_dict']['reference_source']['gene_list_filename']
+ create_symlink = params['param_dict']['reference_source']['create_symlink']
+ print "Canonical gene list file name: %s" % filename
+ print "Create symlink: %s" % create_symlink
+ target_filename = os.path.join(target_dir,os.path.basename(filename))
+ if create_symlink == 'copy_file':
+ shutil.copyfile(filename,target_filename)
+ else:
+ os.symlink(filename,target_filename)
+ # Check identifier and description
+ if not description:
+ description = "%s: %s" % (dbkey,
+ os.path.splitext(os.path.basename(filename))[0])
+ if not identifier:
+ identifier = "%s_%s" % (dbkey,
+ os.path.splitext(os.path.basename(filename))[0])
+ # Update the output dictionary
+ data_manager_dict['data_tables']['rnachipintegrator_canonical_genes'] = {
+ 'value': identifier,
+ 'dbkey': dbkey,
+ 'name': description,
+ 'path': os.path.basename(filename),
+ }
+ elif method == 'history':
+ # Copy file from history
+ filename = params['param_dict']['reference_source']['input_gene_list']
+ target_filename = os.path.join(target_dir,os.path.basename(filename))
+ shutil.copyfile(filename,target_filename)
+ # Check identifier and description
+ if not description:
+ description = "%s: %s" % (dbkey,
+ os.path.splitext(os.path.basename(filename))[0])
+ if not identifier:
+ identifier = "%s_%s" % (dbkey,
+ os.path.splitext(os.path.basename(filename))[0])
+ # Update the output dictionary
+ data_manager_dict['data_tables']['rnachipintegrator_canonical_genes'] = {
+ 'value': identifier,
+ 'dbkey': dbkey,
+ 'name': description,
+ 'path': os.path.basename(filename),
+ }
+ else:
+ raise NotImplementedError("Method '%s' not implemented" % method)
+
+ #save info to json file
+ open(jsonfile,'wb').write(to_json_string(data_manager_dict))
+
diff -r 000000000000 -r 0abe6bac47a6 data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,90 @@
+
+ Fetch and install canonical gene lists for RnaChipIntegrator
+ data_manager_rnachipintegrator_fetch_canonical_genes.py
+ "${out_file}"
+ "${description}"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+**What it does**
+
+Adds a canonical gene list file to the *rnachipintegrator_canonical_genes*
+data table, so that it can be used in the *Analyse canonical genes against ChIP
+data* tool.
+
+At present the gene list files must be created manually and placed on the
+Galaxy server; see below for information on how to obtain canonical gene lists
+from UCSC.
+
+**Notice:** If you leave the description blank then it will be generated
+automatically.
+
+------
+
+.. class:: infomark
+
+**Obtaining canonical gene lists**
+
+Getting canonical gene info from UCSC is covered in the screencast at
+http://blog.openhelix.eu/?p=6097
+
+**UCSC genome browser:** if multiple versions of each gene are visible (e.g.
+if you view 'human Feb 2009 GRCh37/hg19' positions chr17:41,100,000-41,300,000)
+then:
+
+ - Scroll down to the *Gene & Gene Prediction* section
+ - Click on the *UCSC genes* link
+ - Uncheck the tickbox next to *splice variants* and resubmit to view without
+ duplicates.
+
+**UCSC table browser:** to obtain the canonical set of genes from the table browser:
+
+ - Select *knownCanonical* from the table menu
+ - Select selected fields from primary & related tables from the output format menu
+ - Click on *Get output*
+ - Select the fields of interest (e.g. 'chrom', 'chromStart', 'chromEnd' from the
+ 'knownCanonical' table plus 'geneSymbol' from the *kgXref* table.)
+ - Click on Get output to get the data for download
+
+**Hint:** to also get strand direction information i.e. +/-, also allow selection
+from the refGene table, and select the strand field.)
+
+
diff -r 000000000000 -r 0abe6bac47a6 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 0abe6bac47a6 install_tool_deps.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/install_tool_deps.sh Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,64 @@
+#!/bin/bash -e
+#
+# Install the tool dependencies for RnaChipIntegrator for testing from command line
+#
+# Installation directory
+TOP_DIR=$1
+if [ -z "$TOP_DIR" ] ; then
+ echo Usage: $(basename $0) DIR
+ exit
+fi
+if [ -z "$(echo $TOP_DIR | grep ^/)" ] ; then
+ TOP_DIR=$(pwd)/$TOP_DIR
+fi
+if [ ! -d "$TOP_DIR" ] ; then
+ mkdir -p $TOP_DIR
+fi
+cd $TOP_DIR
+# RnaChipIntegrator 1.0.0
+VERSION=1.0.0
+INSTALL_DIR=$TOP_DIR/rnachipintegrator/$VERSION
+mkdir -p $INSTALL_DIR
+wd=$(mktemp -d)
+pushd $wd
+wget https://pypi.python.org/packages/source/R/RnaChipIntegrator/RnaChipIntegrator-${VERSION}.tar.gz
+tar zxf RnaChipIntegrator-${VERSION}.tar.gz
+cd RnaChipIntegrator-$VERSION
+pip install --no-use-wheel --install-option "--prefix=$INSTALL_DIR" .
+popd
+rm -rf $wd/*
+rmdir $wd
+cat > rnachipintegrator/$VERSION/env.sh < xlsxwriter/0.8.4/env.sh <&2
+ echo Creating tool dependencies dir
+ mkdir -p $TOOL_DEPENDENCIES_DIR
+ echo Installing tool dependencies
+ $(dirname $0)/install_tool_deps.sh $TOOL_DEPENDENCIES_DIR
+fi
+# Load dependencies
+for dep in $TOOL_DEPENDENCIES ; do
+ env_file=$TOOL_DEPENDENCIES_DIR/$dep/env.sh
+ if [ -e $env_file ] ; then
+ . $env_file
+ else
+ echo ERROR no env.sh file found for $dep >&2
+ exit 1
+ fi
+done
+#
+# rnachipintegrator_canonical_genes
+#
+# Test #1
+RnaChipIntegrator --name=mm9 \
+ --cutoff=50000 \
+ --number=4 \
+ --xlsx \
+ --compact \
+ test-data/mm9_canonical_genes.tsv test-data/mm9_summits.txt
+mv mm9_gene_centric.txt test-data/mm9_summits_per_feature.out
+mv mm9_peak_centric.txt test-data/mm9_features_per_summit.out
+mv mm9.xlsx test-data/mm9_summits.xlsx
+#
+# Test #2
+RnaChipIntegrator --name=mm9 \
+ --cutoff=50000 \
+ --number=4 \
+ --xlsx \
+ --compact \
+ test-data/mm9_canonical_genes.tsv test-data/mm9_peaks.txt
+mv mm9_gene_centric.txt test-data/mm9_peaks_per_feature1.out
+mv mm9_peak_centric.txt test-data/mm9_features_per_peak1.out
+mv mm9.xlsx test-data/mm9_peaks1.xlsx
+#
+# Test #3
+RnaChipIntegrator --name=mm9 \
+ --cutoff=50000 \
+ --number=4 \
+ --xlsx \
+ --summary \
+ --pad \
+ test-data/mm9_canonical_genes.tsv test-data/mm9_peaks.txt
+mv mm9_gene_centric.txt test-data/mm9_peaks_per_feature3.out
+mv mm9_peak_centric.txt test-data/mm9_features_per_peak3.out
+mv mm9_gene_centric_summary.txt test-data/mm9_peaks_per_feature3.summary
+mv mm9_peak_centric_summary.txt test-data/mm9_features_per_peak3.summary
+mv mm9.xlsx test-data/mm9_peaks3.xlsx
+#
+# rnachipintegrator_wrapper
+#
+# Test #1
+RnaChipIntegrator --name=test \
+ --cutoff=130000 \
+ --number=4 \
+ --promoter_region=-10000,2500 \
+ --xlsx \
+ --compact \
+ test-data/features.txt test-data/summits.txt
+mv test_gene_centric.txt test-data/summits_per_feature.out
+mv test_peak_centric.txt test-data/features_per_summit.out
+mv test.xlsx test-data/summits.xlsx
+#
+# Test #2
+RnaChipIntegrator --name=test \
+ --cutoff=130000 \
+ --number=4 \
+ --promoter_region=-10000,2500 \
+ --xlsx \
+ --compact \
+ test-data/features.txt test-data/peaks.txt
+mv test_gene_centric.txt test-data/peaks_per_feature1.out
+mv test_peak_centric.txt test-data/features_per_peak1.out
+mv test.xlsx test-data/peaks1.xlsx
+#
+# Test #3
+RnaChipIntegrator --name=test \
+ --cutoff=130000 \
+ --number=4 \
+ --xlsx \
+ test-data/features.txt test-data/peaks.txt
+mv test_gene_centric.txt test-data/peaks_per_feature2.out
+mv test_peak_centric.txt test-data/features_per_peak2.out
+mv test.xlsx test-data/peaks2.xlsx
+#
+# Test #4
+RnaChipIntegrator --name=test \
+ --cutoff=130000 \
+ --number=4 \
+ --only-DE \
+ --xlsx \
+ --compact \
+ test-data/features.txt test-data/peaks.txt
+mv test_gene_centric.txt test-data/peaks_per_feature3.out
+mv test_peak_centric.txt test-data/features_per_peak3.out
+mv test.xlsx test-data/peaks3.xlsx
+#
+# Test #5
+RnaChipIntegrator --name=test \
+ --cutoff=130000 \
+ --number=4 \
+ --xlsx \
+ --summary \
+ --pad \
+ test-data/features.txt test-data/peaks.txt
+mv test_gene_centric.txt test-data/peaks_per_feature4.out
+mv test_peak_centric.txt test-data/features_per_peak4.out
+mv test_gene_centric_summary.txt test-data/peaks_per_feature4.summary
+mv test_peak_centric_summary.txt test-data/features_per_peak4.summary
+mv test.xlsx test-data/peaks4.xlsx
+##
+#
diff -r 000000000000 -r 0abe6bac47a6 make_test_data/features.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/make_test_data/features.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,957 @@
+#RefSeq_Gene Symbol chr1 start stop strand diff_exp
+AF064749_Col6a3 chr1 92566771 92800755 - 1
+AK015559_4930472D16Rik chr1 25020851 25021989 - 1
+AK030377_A330023F24Rik chr1 196781953 196826186 - 1
+AK080193_A530079E22Rik chr1 89401837 89403491 - 1
+AK082264_C230030N03Rik chr1 34735043 34781084 + 1
+BC006931_AI597479 chr1 43153807 43172843 + 1
+BC021773_Glb1l chr1 75193364 75207353 - 1
+BC023951_D1Ertd622e chr1 99540054 99558631 - 1
+BC028767_3110009E18Rik chr1 122017764 122114603 + 1
+BC031781_BC031781 chr1 182781250 182798240 + 1
+BC034187_BC035947 chr1 78493611 78497758 - 1
+BC043098_Fam168b chr1 34870072 34917183 - 1
+BC049091_D1Bwg0212e chr1 39592545 39603734 + 1
+BC049713_Ankrd45 chr1 163072817 163099826 + 1
+BC050813_4921511C04Rik chr1 37157481 37244861 + 1
+BC051128_4921521F21Rik chr1 65059273 65079312 - 1
+BC052693_2810422O20Rik chr1 165924541 165927371 + 1
+BC052931_A630001G21Rik chr1 87601462 87674840 - 1
+BC053100_5730559C18Rik chr1 138110108 138130841 - 1
+BC054802_9630058J23Rik chr1 181476521 181558044 + 1
+BC055845_2810025M15Rik chr1 159342483 159350353 + 1
+BC055955_A130010J15Rik chr1 194999663 195004015 + 1
+BC057872_Rab3gap2 chr1 187028006 187110623 + 1
+BC058417_2610017I09Rik chr1 42648822 42751667 - 1
+BC059254_Phlpp chr1 108042052 108306367 + 1
+BC070435_Fam123c chr1 34620070 34671545 + 1
+BC070446_Fam135a chr1 24017617 24107170 - 1
+BC071241_9430016H08Rik chr1 57463192 57497936 + 1
+BC072639_2010300C02Rik chr1 37646877 37776659 - 1
+BC080290_5033414K04Rik chr1 84032539 84360735 - 0
+BC082310_9430031J16Rik chr1 81073525 81338329 + 0
+BC089525_2310007B03Rik chr1 95047933 95063386 - 0
+BC089561_Cep350 chr1 157692096 157820375 - 0
+BC147491_A230074B11Rik chr1 37083441 37133840 + 0
+BC147657_9630028B13Rik chr1 187253234 187265698 - 0
+ENSMUST00000027997_Rgs5 chr1 171625108 171625913 + 0
+ENSMUST00000051203_1700001G17Rik chr1 33726669 33727551 + 0
+ENSMUST00000054333_A130050O07Rik chr1 139823828 139826840 + 0
+ENSMUST00000056879_C230029F24Rik chr1 49301475 49397265 + 0
+ENSMUST00000057543_A730013G03Rik chr1 194659323 194661397 - 0
+ENSMUST00000062637_4930470H14Rik chr1 175156866 175201240 + 0
+ENSMUST00000070048_ENSMUSG00000056128 chr1 92571736 92576368 + 0
+ENSMUST00000070987_EG433384 chr1 183781705 183783320 - 0
+ENSMUST00000072395_Olfr1406 chr1 175113651 175120746 - 0
+ENSMUST00000094288_Wdr64 chr1 177654798 177798070 + 0
+ENSMUST00000094950_Pgap1 chr1 54529849 54614539 - 0
+ENSMUST00000097776_Cnnm3 chr1 36567938 36585164 + 0
+EU429481_Igfn1 chr1 137825893 137890307 - 0
+FJ024495_Ildr2 chr1 168236882 168239692 - 0
+FJ210934_Unc80 chr1 66514856 66556109 + 0
+NM_001001565_Chpf chr1 75470923 75476437 - 0
+NM_001001809_Olfr218 chr1 175130421 175134469 + 0
+NM_001001883_Hecw2 chr1 53867026 54252002 - 0
+NM_001003917_Atg9a chr1 75177439 75189181 - 0
+NM_001004173_Sgpp2 chr1 78306692 78416864 + 0
+NM_001005423_Mreg chr1 72170192 72258895 - 0
+NM_001005507_Smg7 chr1 154684125 154750410 - 0
+NM_001005508_Arhgap30 chr1 173319072 173340822 + 0
+NM_001005520_Olfr244 chr1 176032571 176067605 - 0
+NM_001008419_Aox3l1 chr1 58335180 58437083 + 0
+NM_001008426_EG433365 chr1 155721475 155724001 + 0
+NM_001008533_Adora1 chr1 136095799 136181661 - 0
+NM_001009940_Il19 chr1 132786042 132915234 - 0
+NM_001011525_Olfr1415 chr1 94376258 94381054 - 0
+NM_001011525_Olfr1415 chr1 94407669 94418761 - 0
+NM_001011684_Nms chr1 38995917 39007113 + 0
+NM_001011873_Xkr9 chr1 13658862 13691794 + 0
+NM_001011874_Xkr4 chr1 3203722 3713108 - 0
+NM_001012330_Zfp238 chr1 179359958 179380892 + 0
+NM_001013374_Lman2l chr1 36362897 36502078 - 0
+NM_001013382_Lrrc52 chr1 169375806 169397136 - 0
+NM_001013771_Gm973 chr1 59573136 59693241 + 0
+NM_001013779_Aim2 chr1 175385835 175396165 + 0
+NM_001014974_Ttll4 chr1 74708314 74748400 + 0
+NM_001024721_BC094916 chr1 175451304 175466101 - 0
+NM_001024945_Qsox1 chr1 157625296 157670499 - 0
+NM_001025156_Ccdc93 chr1 123208865 123403037 + 0
+NM_001025565_Lhx9 chr1 140694768 140740509 - 0
+NM_001025602_Il1rl1 chr1 40462708 40522260 + 0
+NM_001029984_Fcrlb chr1 172836813 172843072 - 0
+NM_001037170_Tomm40l chr1 173147934 173152645 - 0
+NM_001037725_Fam117b chr1 59937517 60042190 + 0
+NM_001037918_Lipt1 chr1 37928603 37934232 + 0
+NM_001037999_Dbi chr1 122009883 122046068 - 0
+NM_001038592_Glrx2 chr1 145585774 145608282 + 0
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+NR_002840_Gas5 chr1 162964758 162968663 + 0
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diff -r 000000000000 -r 0abe6bac47a6 make_test_data/mm9_canonical_genes.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/make_test_data/mm9_canonical_genes.tsv Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,10 @@
+mm9.kgXref.geneSymbol #mm9.knownCanonical.chrom mm9.knownCanonical.chromStart mm9.knownCanonical.chromEnd mm9.knownGene.strand mm9.knownCanonical.transcript mm9.kgXref.refseq
+Xkr4 chr1 3204562 3661579 - uc007aeu.1 NM_001011874
+AK149000 chr1 3638391 3648985 - uc007aev.1
+Rp1 chr1 4333587 4350395 - uc007aex.2 NM_011283
+Sox17 chr1 4481008 4486494 - uc007aez.1 NM_011441
+Mrpl15 chr1 4763278 4775807 - uc007aff.2 NM_001177658
+Lypla1 chr1 4797973 4836816 + uc007afh.1 NM_008866
+Tcea1 chr1 4847774 4887990 + uc007afi.2 NM_011541
+Rgs20 chr1 4899656 5060366 - uc007afl.2 NM_001177795
+Atp6v1h chr1 5073253 5152630 + uc007afn.1 NM_133826
diff -r 000000000000 -r 0abe6bac47a6 make_test_data/mm9_peaks.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/make_test_data/mm9_peaks.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,500 @@
+chr1 3213477 3213513
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diff -r 000000000000 -r 0abe6bac47a6 make_test_data/mm9_summits.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r 0abe6bac47a6 make_test_data/peaks.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/make_test_data/peaks.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,70 @@
+#peak s e
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diff -r 000000000000 -r 0abe6bac47a6 make_test_data/summits.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/make_test_data/summits.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,654 @@
+#peak mid plus1
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+chr6 51351355 51351356
+chr6 56806957 56806958
+chr6 67253361 67253362
+chr6 76927942 76927943
+chr6 83071812 83071813
+chr6 83093011 83093012
+chr6 86130730 86130731
+chr6 87137073 87137074
+chr6 87222111 87222112
+chr6 94625281 94625282
+chr7 104849801 104849802
+chr7 117975070 117975071
+chr7 119647132 119647133
+chr7 119813749 119813750
+chr7 120393123 120393124
+chr7 120874367 120874368
+chr7 123336714 123336715
+chr7 125720143 125720144
+chr7 126039427 126039428
+chr7 127004913 127004914
+chr7 128854935 128854936
+chr7 128984541 128984542
+chr7 134819118 134819119
+chr7 135696903 135696904
+chr7 137484210 137484211
+chr7 137768001 137768002
+chr7 138009297 138009298
+chr7 138123566 138123567
+chr7 138123699 138123700
+chr7 139426142 139426143
+chr7 146041529 146041530
+chr7 147156352 147156353
+chr7 148379180 148379181
+chr7 148379362 148379363
+chr7 148629281 148629282
+chr7 150571560 150571561
+chr7 152450338 152450339
+chr7 152450519 152450520
+chr7 16562058 16562059
+chr7 16894872 16894873
+chr7 17429367 17429368
+chr7 20044401 20044402
+chr7 26061110 26061111
+chr7 26574315 26574316
+chr7 28010205 28010206
+chr7 30227710 30227711
+chr7 30256558 30256559
+chr7 35861923 35861924
+chr7 56809068 56809069
+chr7 87336398 87336399
+chr7 88092779 88092780
+chr7 89920499 89920500
+chr8 10576464 10576465
+chr8 107426996 107426997
+chr8 109087961 109087962
+chr8 109275046 109275047
+chr8 109334564 109334565
+chr8 113806188 113806189
+chr8 119851483 119851484
+chr8 121354388 121354389
+chr8 129127362 129127363
+chr8 129549456 129549457
+chr8 13548998 13548999
+chr8 13668465 13668466
+chr8 14306960 14306961
+chr8 17594804 17594805
+chr8 19919526 19919527
+chr8 19924810 19924811
+chr8 22870138 22870139
+chr8 23921280 23921281
+chr8 24206095 24206096
+chr8 34068894 34068895
+chr8 37107644 37107645
+chr8 4586605 4586606
+chr8 70850825 70850826
+chr8 71717281 71717282
+chr8 73173598 73173599
+chr8 73183558 73183559
+chr8 73297497 73297498
+chr8 81256455 81256456
+chr8 86143616 86143617
+chr8 87180694 87180695
+chr8 88126748 88126749
+chr8 93828640 93828641
+chr8 97699878 97699879
+chr9 100543647 100543648
+chr9 103988283 103988284
+chr9 106273656 106273657
+chr9 107478162 107478163
+chr9 108851463 108851464
+chr9 110183808 110183809
+chr9 111053664 111053665
+chr9 116828689 116828690
+chr9 118884586 118884587
+chr9 120883928 120883929
+chr9 123371104 123371105
+chr9 13408238 13408239
+chr9 14466849 14466850
+chr9 14480293 14480294
+chr9 24346538 24346539
+chr9 3258857 3258858
+chr9 42777363 42777364
+chr9 43528251 43528252
+chr9 43585984 43585985
+chr9 44215148 44215149
+chr9 44307103 44307104
+chr9 54460731 54460732
+chr9 66728918 66728919
+chr9 66794084 66794085
+chr9 67556540 67556541
+chr9 70477636 70477637
+chr9 72497695 72497696
+chr9 72916030 72916031
+chr9 74815214 74815215
+chr9 75371664 75371665
+chr9 8033087 8033088
+chr9 8055015 8055016
+chr9 83462792 83462793
+chr9 86714892 86714893
+chrX 109484691 109484692
+chrX 137172820 137172821
+chrX 139917606 139917607
+chrX 140401017 140401018
+chrX 163589625 163589626
+chrX 166360754 166360755
+chrX 166427362 166427363
+chrX 166432950 166432951
+chrX 84483714 84483715
+chrX 98516735 98516736
diff -r 000000000000 -r 0abe6bac47a6 package_rnachipintegrator_wrapper.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/package_rnachipintegrator_wrapper.sh Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,32 @@
+#!/bin/sh
+#
+# Package RnaChipIntegrator files into tgz file for upload to
+# Galaxy toolshed
+#
+VERSION=$(grep "@VERSION@" rnachipintegrator_macros.xml | cut -d'>' -f2 | cut -d'<' -f1)
+TGZ=rnachipintegrator-${VERSION}.tgz
+if [ -f $TGZ ] ; then
+ echo $TGZ: already exists, please remove >&2
+ exit 1
+fi
+tar cvzf $TGZ \
+ README.rst \
+ rnachipintegrator_macros.xml \
+ rnachipintegrator_wrapper.xml \
+ rnachipintegrator_canonical_genes.xml \
+ rnachipintegrator_wrapper.sh \
+ tool_dependencies.xml \
+ data_manager \
+ data_manager_conf.xml \
+ tool-data \
+ tool_data_table_conf.xml.sample \
+ test-data \
+ --exclude=*~
+if [ -f $TGZ ] ; then
+ echo Created $TGZ
+else
+ echo Failed to created $TGZ >&2
+ exit 1
+fi
+##
+#
diff -r 000000000000 -r 0abe6bac47a6 rnachipintegrator-1.0.0.tgz
Binary file rnachipintegrator-1.0.0.tgz has changed
diff -r 000000000000 -r 0abe6bac47a6 rnachipintegrator_canonical_genes.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnachipintegrator_canonical_genes.xml Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,202 @@
+
+ using RnaChipIntegrator
+
+ rnachipintegrator_macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ output['compact_format'] is False
+ output['summary'] is True
+
+
+ output['compact_format'] is False
+ output['summary'] is True
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+**What it does**
+
+Performs integrated analyses of a set of peaks (e.g. ChIP data) against a
+list of "canonical genes" for a specific organism and genome build,
+identifying the nearest peaks to each canonical gene (and vice versa).
+
+RnaChipIntegrator can be obtained from
+http://fls-bioinformatics-core.github.com/RnaChipIntegrator/
+
+-------------
+
+.. class:: infomark
+
+**Input**
+
+The peak data must be in a tabular file with at least 3 columns of data
+for each peak (one peak per line):
+
+====== ========== =================================
+Column Name Description
+====== ========== =================================
+ 1 chr Chromosome name
+ 2 start Start position of the peak
+ 3 end End position of the peak
+====== ========== =================================
+
+-------------
+
+.. class:: infomark
+
+**Outputs**
+
+The key outputs from the tool are two lists compromising the nearest
+peaks for each gene, and the nearest gene for each peak (one
+dataset for each list).
+
+There are two formats for reporting: "compact" and "full":
+
+ * **Compact output** reports all the hits for each peak or gene on
+ a single line of output;
+ * **Full output** reports each peak/gene pair on a separate line
+ (i.e. a multi-line output format).
+
+In "full" output mode, additional options are available:
+
+ * The output files can be "padded" with extra (empty) lines to ensure
+ that there are always the same number of lines for each peak or
+ gene, if fewer than the requested number of hits are found.
+ * "Summary" datasets can also be requested, which include just the
+ nearest peak reported for each gene (and vice versa).
+
+In either mode these data will also be output in a single MS Excel file,
+which contains one sheet per result set.
+
+.. class:: warning
+
+Using "compact" output with the number of hits limited to more than 4
+peak/gene pairs (or with no limit at all) can result in a large number
+of columns in the output files, which in some versions of Galaxy will
+not be properly displayed. However the data files themselves should be
+okay.
+
+-------------
+
+.. class:: informark
+
+**More information**
+
+It is recommended that you refer to the ``RnaChipIntegrator``
+documentation for information on the contents of each output file:
+
+* http://rnachipintegrator.readthedocs.org/en/latest/
+
+-------------
+
+.. class:: infomark
+
+**Credits**
+
+This Galaxy tool has been developed within the Bioinformatics Core Facility at the
+University of Manchester. It runs the RnaChipIntegrator package which has also been
+developed by this group, and is documented at
+https://pypi.python.org/pypi/RnaChipIntegrator/
+
+Please kindly acknowledge the Bioinformatics Core Facility if you use this tool.
+
+
+
diff -r 000000000000 -r 0abe6bac47a6 rnachipintegrator_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnachipintegrator_macros.xml Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,68 @@
+
+ 1.0.0
+
+
+ python_xlsxwriter
+ rnachipintegrator
+
+
+
+ RnaChipIntegrator --version
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @misc{Briggs2016,
+ author = {Briggs PJ, Donaldson IJ, Zeef LAH},
+ title = {RnaChipIntegrator},
+ publisher = {GitHub},
+ journal = {GitHub repository},
+ year = {2016},
+ howpublished = {\url{https://github.com/fls-bioinformatics-core/RnaChipIntegrator}},
+ version = {1.0.0}
+}
+
+
+
diff -r 000000000000 -r 0abe6bac47a6 rnachipintegrator_wrapper.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnachipintegrator_wrapper.sh Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,105 @@
+#!/bin/sh
+#
+# Wrapper script to run RnaChipIntegrator as a Galaxy tool
+#
+# usage: sh rnachipintegrator_wrapper.sh [OPTIONS] --output_xls
+#
+echo RnaChipIntegrator: analyse gene and peak data
+#
+# Collect command line options
+opts=
+xlsx_file=
+zip_file=
+gene_centric=
+peak_centric=
+gene_centric_summary=
+peak_centric_summary=
+while [ ! -z "$1" ] ; do
+ case $1 in
+ --xlsx_file)
+ shift; xlsx_file=$1
+ opts="$opts --xlsx"
+ ;;
+ --output_files)
+ shift; gene_centric=$1
+ shift; peak_centric=$1
+ ;;
+ --summary_files)
+ shift; gene_centric_summary=$1
+ shift; peak_centric_summary=$1
+ opts="$opts --summary"
+ ;;
+ --zip_file)
+ shift; zip_file=$1
+ ;;
+ *)
+ opts="$opts $1"
+ ;;
+ esac
+ shift
+done
+#
+# Run RnaChipIntegrator
+# NB append stderr to stdout otherwise Galaxy job will fail
+# Direct output to a temporary directory
+outdir=$(mktemp -d)
+base_name=galaxy
+cmd="RnaChipIntegrator --name=${outdir}/${base_name} $opts"
+echo $cmd
+$cmd 2>&1
+#
+# Check exit code
+exit_status=$?
+if [ "$exit_status" -ne "0" ] ; then
+ echo RnaChipIntegrator exited with non-zero status >&2
+ # Clean up and exit
+ /bin/rm -rf $outdir
+ exit $exit_status
+fi
+#
+# Deal with output XLSX file
+if [ -f "${outdir}/${base_name}.xlsx" ] ; then
+ /bin/mv ${outdir}/${base_name}.xlsx $xlsx_file
+else
+ echo No file ${outdir}/${base_name}.xlsx >&2
+ # Clean up and exit
+ /bin/rm -rf $outdir
+ exit 1
+fi
+#
+# Generate zip file
+if [ ! -z "$zip_file" ] ; then
+ for ext in \
+ gene_centric \
+ gene_centric_summary \
+ peak_centric \
+ peak_centric_summary ; do
+ txt_file=${outdir}/${base_name}_${ext}.txt
+ if [ -f "$txt_file" ] ; then
+ zip -j -g ${outdir}/archive.zip $txt_file
+ fi
+ done
+ /bin/mv ${outdir}/archive.zip $zip_file
+fi
+#
+# Collect tab delimited files
+for ext in \
+ gene_centric \
+ gene_centric_summary \
+ peak_centric \
+ peak_centric_summary ; do
+ eval dest=\$$ext
+ if [ ! -z "$dest" ] ; then
+ outfile=${outdir}/${base_name}_${ext}.txt
+ if [ -f "$outfile" ] ; then
+ /bin/mv $outfile $dest
+ else
+ echo ERROR missing output file $outfile >&2
+ fi
+ fi
+done
+#
+# Clean up
+/bin/rm -rf $outdir
+#
+# Done
diff -r 000000000000 -r 0abe6bac47a6 rnachipintegrator_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnachipintegrator_wrapper.xml Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,264 @@
+
+
+ Integrated analysis of 'gene' and 'peak' data
+
+ rnachipintegrator_macros.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ output['compact_format'] is False
+ output['summary'] is True
+
+
+ output['compact_format'] is False
+ output['summary'] is True
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+**What it does**
+
+Performs integrated analyses of genes (or other genomic feature data)
+gainst a set of peaks (e.g. ChIP data), identifying the nearest peaks to
+each feature and vice versa.
+
+The program was originally written specifically for ChIP-Seq and RNA-Seq
+data but works equally well for ChIP-chip and microarray expression data,
+and can also be used to integrate any set of genomic features (e.g.
+canonical genes, CpG islands) with expression data.
+
+RnaChipIntegrator can be obtained from
+https://pypi.python.org/pypi/RnaChipIntegrator/
+
+-------------
+
+.. class:: infomark
+
+**Input**
+
+The gene data must be in a tabular file with the following columns
+of data for each gene or genomic feature (one gene per line):
+
+====== ========== ======================================================================
+Column Name Description
+====== ========== ======================================================================
+ 1 ID Name used to identify the gene in the output
+ 2 chr Chromosome name
+ 3 start Start position of the gene
+ 4 end End position of the gene
+ 5 strand Must be either '+' or '-'
+ 6 diff_expr Optional: indicates gene is differentially expressed (1) or not (0)
+====== ========== ======================================================================
+
+The peak data must be in a tabular file with at least 3 columns of data
+for each peak (one peak per line):
+
+====== ========== =================================
+Column Name Description
+====== ========== =================================
+ 1 chr Chromosome name
+ 2 start Start position of the peak
+ 3 end End position of the peak
+====== ========== =================================
+
+If peak data is in ``bed`` format then the tool will automatically
+assign the correct columns, otherwise the first three columns of data
+will be used.
+
+-------------
+
+.. class:: infomark
+
+**Outputs**
+
+The key outputs from the tool are two lists compromising the nearest
+peaks for each gene, and the nearest gene for each peak (one dataset
+for each list).
+
+There are two formats for reporting: "compact" and "full":
+
+ * **Compact output** reports all the hits for each peak or gene on
+ a single line of output;
+ * **Full output** reports each peak/gene pair on a separate line
+ (i.e. a multi-line output format).
+
+In "full" output mode, additional options are available:
+
+ * The output files can be "padded" with extra (empty) lines to ensure
+ that there are always the same number of lines for each peak or
+ gene, if fewer than the requested number of hits are found.
+ * "Summary" datasets can also be requested, which include just the
+ nearest peak reported for each gene (and vice versa).
+
+In either mode these data will also be output in a single MS Excel file,
+which contains one sheet per result set.
+
+.. class:: warning
+
+Using "compact" output with the number of hits limited to more than 4
+peak/gene pairs (or with no limit at all) can result in a large number
+of columns in the output files, which in some versions of Galaxy will
+not be properly displayed. However the data files themselves should be
+okay.
+
+-------------
+
+.. class:: informark
+
+**More information**
+
+It is recommended that you refer to the ``RnaChipIntegrator``
+documentation for information on the contents of each output file:
+
+* http://rnachipintegrator.readthedocs.org/en/latest/
+
+-------------
+
+.. class:: infomark
+
+**Credits**
+
+This Galaxy tool has been developed within the Bioinformatics Core Facility at the
+University of Manchester. It runs the RnaChipIntegrator package which has also been
+developed by this group, and is documented at
+http://fls-bioinformatics-core.github.com/RnaChipIntegrator/
+
+Please kindly acknowledge the Bioinformatics Core Facility if you use this tool.
+
+
+
diff -r 000000000000 -r 0abe6bac47a6 run_planemo_tests.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/run_planemo_tests.sh Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,43 @@
+#!/bin/bash
+#
+# Install dependencies and set up environment for
+# rnachipintegrator tool, then run tests using planemo
+#
+# Note that any arguments supplied to the script are
+# passed directly to the "planemo test..." invocation
+#
+# e.g. --install_galaxy (to get planemo to create a
+# Galaxy instance to run tests)
+#
+# --galaxy_root DIR (to run tests using existing
+# Galaxy instance)
+#
+# List of dependencies
+TOOL_DEPENDENCIES="rnachipintegrator/1.0.0
+ xlsxwriter/0.8.4"
+# Where to find them
+TOOL_DEPENDENCIES_DIR=$(pwd)/test.tool_dependencies.rnachipintegrator
+if [ ! -d $TOOL_DEPENDENCIES_DIR ] ; then
+ echo WARNING $TOOL_DEPENDENCIES_DIR not found >&2
+ echo Creating tool dependencies dir
+ mkdir -p $TOOL_DEPENDENCIES_DIR
+ echo Installing tool dependencies
+ $(dirname $0)/install_tool_deps.sh $TOOL_DEPENDENCIES_DIR
+fi
+# Load dependencies
+for dep in $TOOL_DEPENDENCIES ; do
+ env_file=$TOOL_DEPENDENCIES_DIR/$dep/env.sh
+ if [ -e $env_file ] ; then
+ . $env_file
+ else
+ echo ERROR no env.sh file found for $dep >&2
+ exit 1
+ fi
+done
+# Run the planemo tests
+planemo test $@ \
+ $(dirname $0)/rnachipintegrator_wrapper.xml \
+ $(dirname $0)/rnachipintegrator_canonical_genes.xml \
+ $(dirname $0)/data_manager/data_manager_rnachipintegrator_fetch_canonical_genes.xml
+##
+#
diff -r 000000000000 -r 0abe6bac47a6 test-data/features.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,957 @@
+#RefSeq_Gene Symbol chr1 start stop strand diff_exp
+AF064749_Col6a3 chr1 92566771 92800755 - 1
+AK015559_4930472D16Rik chr1 25020851 25021989 - 1
+AK030377_A330023F24Rik chr1 196781953 196826186 - 1
+AK080193_A530079E22Rik chr1 89401837 89403491 - 1
+AK082264_C230030N03Rik chr1 34735043 34781084 + 1
+BC006931_AI597479 chr1 43153807 43172843 + 1
+BC021773_Glb1l chr1 75193364 75207353 - 1
+BC023951_D1Ertd622e chr1 99540054 99558631 - 1
+BC028767_3110009E18Rik chr1 122017764 122114603 + 1
+BC031781_BC031781 chr1 182781250 182798240 + 1
+BC034187_BC035947 chr1 78493611 78497758 - 1
+BC043098_Fam168b chr1 34870072 34917183 - 1
+BC049091_D1Bwg0212e chr1 39592545 39603734 + 1
+BC049713_Ankrd45 chr1 163072817 163099826 + 1
+BC050813_4921511C04Rik chr1 37157481 37244861 + 1
+BC051128_4921521F21Rik chr1 65059273 65079312 - 1
+BC052693_2810422O20Rik chr1 165924541 165927371 + 1
+BC052931_A630001G21Rik chr1 87601462 87674840 - 1
+BC053100_5730559C18Rik chr1 138110108 138130841 - 1
+BC054802_9630058J23Rik chr1 181476521 181558044 + 1
+BC055845_2810025M15Rik chr1 159342483 159350353 + 1
+BC055955_A130010J15Rik chr1 194999663 195004015 + 1
+BC057872_Rab3gap2 chr1 187028006 187110623 + 1
+BC058417_2610017I09Rik chr1 42648822 42751667 - 1
+BC059254_Phlpp chr1 108042052 108306367 + 1
+BC070435_Fam123c chr1 34620070 34671545 + 1
+BC070446_Fam135a chr1 24017617 24107170 - 1
+BC071241_9430016H08Rik chr1 57463192 57497936 + 1
+BC072639_2010300C02Rik chr1 37646877 37776659 - 1
+BC080290_5033414K04Rik chr1 84032539 84360735 - 0
+BC082310_9430031J16Rik chr1 81073525 81338329 + 0
+BC089525_2310007B03Rik chr1 95047933 95063386 - 0
+BC089561_Cep350 chr1 157692096 157820375 - 0
+BC147491_A230074B11Rik chr1 37083441 37133840 + 0
+BC147657_9630028B13Rik chr1 187253234 187265698 - 0
+ENSMUST00000027997_Rgs5 chr1 171625108 171625913 + 0
+ENSMUST00000051203_1700001G17Rik chr1 33726669 33727551 + 0
+ENSMUST00000054333_A130050O07Rik chr1 139823828 139826840 + 0
+ENSMUST00000056879_C230029F24Rik chr1 49301475 49397265 + 0
+ENSMUST00000057543_A730013G03Rik chr1 194659323 194661397 - 0
+ENSMUST00000062637_4930470H14Rik chr1 175156866 175201240 + 0
+ENSMUST00000070048_ENSMUSG00000056128 chr1 92571736 92576368 + 0
+ENSMUST00000070987_EG433384 chr1 183781705 183783320 - 0
+ENSMUST00000072395_Olfr1406 chr1 175113651 175120746 - 0
+ENSMUST00000094288_Wdr64 chr1 177654798 177798070 + 0
+ENSMUST00000094950_Pgap1 chr1 54529849 54614539 - 0
+ENSMUST00000097776_Cnnm3 chr1 36567938 36585164 + 0
+EU429481_Igfn1 chr1 137825893 137890307 - 0
+FJ024495_Ildr2 chr1 168236882 168239692 - 0
+FJ210934_Unc80 chr1 66514856 66556109 + 0
+NM_001001565_Chpf chr1 75470923 75476437 - 0
+NM_001001809_Olfr218 chr1 175130421 175134469 + 0
+NM_001001883_Hecw2 chr1 53867026 54252002 - 0
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+NM_146103_Tmem185b chr1 121396063 121425550 + 0
+NM_146106_Lyplal1 chr1 187911630 187941208 - 0
+NM_146107_Actr1b chr1 36754975 36766847 - 0
+NM_146108_Hibch chr1 52899113 52977830 + 0
+NM_146110_Aamp chr1 74326421 74331613 - 0
+NM_146112_Gigyf2 chr1 89223593 89347370 + 0
+NM_146250_Gpr1 chr1 63229165 63309823 - 0
+NM_146277_Olfr1412 chr1 94484843 94486082 + 0
+NM_146305_Olfr420 chr1 176088784 176089871 + 0
+NM_146490_Olfr1411 chr1 94493008 94494065 + 0
+NM_146491_Olfr1410 chr1 94504416 94505384 + 0
+NM_146715_Olfr419 chr1 176180115 176200418 - 0
+NM_146716_Olfr432 chr1 175977437 175981444 + 0
+NM_146717_Olfr433 chr1 175971174 175973629 + 0
+NM_146718_Olfr430 chr1 175999350 176000384 + 0
+NM_146720_Olfr421 chr1 176072364 176082596 + 0
+NM_146721_Olfr424 chr1 176057388 176067824 + 0
+NM_146722_Olfr429 chr1 176019173 176020111 + 0
+NM_146761_Olfr414 chr1 176360513 176361670 + 0
+NM_146764_Olfr1408 chr1 175060414 175083388 - 0
+NM_146881_Olfr1404 chr1 175145784 175146725 + 0
+NM_147037_Olfr1413 chr1 94469750 94470721 + 0
+NM_148937_Plcd4 chr1 74589462 74614368 + 0
+NM_152895_Kdm5b chr1 136455975 136529487 + 0
+NM_152915_Dner chr1 84366415 84706993 - 0
+NM_153064_Ndufs2 chr1 173164989 173180188 - 0
+NM_153088_Ctdsp1 chr1 74438065 74443852 + 0
+NM_153111_Fev chr1 74915158 74932371 - 0
+NM_153114_Otos chr1 94540797 94553072 - 0
+NM_153137_Traf3ip3 chr1 195001656 195027877 - 0
+NM_153154_Tcfap2d chr1 19027377 19157044 + 0
+NM_153171_Rgs13 chr1 145985803 146024550 - 0
+NM_153179_Pkhd1 chr1 20040166 20661582 - 0
+NM_153408_Neurl3 chr1 36321504 36355139 - 0
+NM_153502_Ankrd23 chr1 36587038 36593708 - 0
+NM_153530_Dis3l2 chr1 88570607 88946671 + 0
+NM_153539_Fam5c chr1 148341910 148749599 + 0
+NM_153555_Wdr42a chr1 174078166 174127554 + 0
+NM_153556_Pms1 chr1 53245508 53353841 - 0
+NM_153601_Lgsn chr1 31221394 31261688 + 0
+NM_153744_Prkag3 chr1 74785516 74825109 - 0
+NM_153774_Ipo9 chr1 137278207 137330146 - 0
+NM_170597_Creg2 chr1 39677083 39708307 - 0
+NM_170755_Fam134a chr1 75137484 75144869 + 0
+NM_172054_Txndc9 chr1 38041434 38054101 - 0
+NM_172124_B3gat2 chr1 23755411 23855977 + 0
+NM_172294_Sulf1 chr1 12708560 12851249 + 0
+NM_172406_Trak2 chr1 58955979 59031177 - 0
+NM_172422_Fastkd2 chr1 63777134 63803028 + 0
+NM_172430_Sphkap chr1 83207585 83404745 - 0
+NM_172463_Sned1 chr1 95132418 95197642 + 0
+NM_172484_E030049G20Rik chr1 127810213 128389504 - 0
+NM_172485_Thsd7b chr1 131169889 132172070 + 0
+NM_172499_Mfsd9 chr1 40828883 40921070 - 0
+NM_172510_Mfsd4 chr1 133919383 133964629 - 0
+NM_172513_Fam126b chr1 58575029 58643157 - 0
+NM_172516_Dstyk chr1 134314046 134363525 + 0
+NM_172517_Rbbp5 chr1 134368568 134402423 + 0
+NM_172643_Zbtb41 chr1 141318960 141349577 + 0
+NM_172644_Dars2 chr1 162970732 163001279 - 0
+NM_172647_F11r chr1 173365700 173394971 + 0
+NM_172648_Ifi205 chr1 175664572 175958593 - 0
+NM_172650_Kctd3 chr1 190794974 190831710 - 0
+NM_172652_4632411B12Rik chr1 36381585 36426026 - 0
+NM_172653_Slc39a10 chr1 46863572 46949677 - 0
+NM_172656_Stradb chr1 59012025 59052817 + 0
+NM_172841_Slco5a1 chr1 12857471 12982812 - 0
+NM_172843_Tor1aip2 chr1 157906541 157915942 + 0
+NM_172844_Fmo9 chr1 168589849 168611976 - 0
+NM_172845_Adamts4 chr1 173178880 173192383 + 0
+NM_172846_Dnahc14 chr1 183669052 183694102 + 0
+NM_172850_Ankmy1 chr1 94757771 94799473 - 0
+NM_172851_Cntnap5b chr1 101934704 102382815 + 0
+NM_172852_Serpinb13 chr1 108877561 108897772 + 0
+NM_172853_Cdh7 chr1 111718165 112036714 + 0
+NM_172974_Cops7b chr1 88478926 88503950 + 0
+NM_173029_Adcy10 chr1 167415324 167506904 + 0
+NM_173187_2310035C23Rik chr1 107560448 107651751 + 0
+NM_173378_Trp53bp2 chr1 184333536 184392728 + 0
+NM_173395_Fam132b chr1 93263007 93270794 + 0
+NM_173424_Zbtb37 chr1 162938038 162965197 - 0
+NM_173425_Fam124b chr1 80156958 80214611 - 0
+NM_173437_Nav1 chr1 137332309 137482282 - 0
+NM_173437_Nav1 chr1 137481360 137496527 + 0
+NM_173443_Vcpip1 chr1 9709587 9764569 - 0
+NM_173760_Hisppd1 chr1 99592475 99667685 - 0
+NM_173771_4933406M09Rik chr1 136282517 136287560 + 0
+NM_173772_Neu4 chr1 95917070 95928707 + 0
+NM_173865_Slc41a1 chr1 133724090 133745438 + 0
+NM_173868_St18 chr1 6477297 6885001 + 0
+NM_173870_Mgat4a chr1 37496234 37609425 - 0
+NM_174874_Atg4b chr1 95648097 95687167 + 0
+NM_174985_Gpbar1 chr1 74321873 74326272 + 0
+NM_175031_Stk36 chr1 74648039 74683468 + 0
+NM_175106_Tmem177 chr1 121793019 121809709 - 0
+NM_175118_Dusp28 chr1 94803563 94805012 + 0
+NM_175127_Fbxo28 chr1 184242976 184303818 - 0
+NM_175170_Pogk chr1 168314763 168391350 - 0
+NM_175200_Als2cr11 chr1 59053967 59151744 - 0
+NM_175210_Abca12 chr1 71207671 71501632 - 0
+NM_175236_Adhfe1 chr1 9538049 9570746 + 0
+NM_175259_Shisa4 chr1 137267654 137274885 - 0
+NM_175293_D630023F18Rik chr1 65151863 65176420 - 0
+NM_175294_Nucks1 chr1 133807079 133832888 + 0
+NM_175296_Mael chr1 168115771 168178081 - 0
+NM_175370_Als2cr12 chr1 58714975 58752801 - 0
+NM_175382_2700049P18Rik chr1 133344141 133436449 + 0
+NM_175439_Mars2 chr1 55294084 55297625 + 0
+NM_175443_Etnk2 chr1 135260167 135276893 + 0
+NM_175460_Nmnat2 chr1 154802128 154966391 + 0
+NM_175461_Fam78b chr1 168898096 169021408 + 0
+NM_175564_Tmem169 chr1 72330953 72349677 + 0
+NM_175642_Bai3 chr1 25084207 25887514 - 0
+NM_175686_Prrx1 chr1 165175252 165245859 - 0
+NM_176916_Pld5 chr1 177892457 178205403 - 0
+NM_176972_Usp37 chr1 74482084 74590860 - 0
+NM_176980_Ankar chr1 72689581 72747143 - 0
+NM_177068_Olfml2b chr1 172569075 172612915 + 0
+NM_177084_Slc9a4 chr1 40636956 40687551 + 0
+NM_177129_Cntn2 chr1 134406005 134442705 - 0
+NM_177164_A830006F12Rik chr1 70772309 70929065 + 0
+NM_177173_A830018L16Rik chr1 11404178 11994163 + 0
+NM_177235_Bend6 chr1 33903283 33964764 - 0
+NM_177243_Slc26a9 chr1 133640599 133668075 + 0
+NM_177305_Arl4c chr1 90569702 90617572 - 0
+NM_177397_Atp6v1g3 chr1 140120875 140186039 + 0
+NM_177445_Dars chr1 130260284 130314013 - 0
+NM_177587_Aqp12 chr1 94886487 94908846 + 0
+NM_177604_AA986860 chr1 132628563 132644539 + 0
+NM_177643_Zfp281 chr1 138487073 138526617 + 0
+NM_177646_Dgkd chr1 89749836 89841946 + 0
+NM_177722_6030422M02Rik chr1 9898713 9932156 + 0
+NM_177723_Vsig8 chr1 174486069 174513273 + 0
+NM_177724_D230039L06Rik chr1 180426979 180686112 + 0
+NM_177756_Glt25d2 chr1 154223175 154357825 + 0
+NM_177757_Kif26b chr1 180720593 180862983 + 0
+NM_177781_Trpa1 chr1 14861962 14909072 - 0
+NM_177834_Cpa6 chr1 10314801 10710026 - 0
+NM_177838_Fam163a chr1 157923096 158135544 - 0
+NM_177839_Tnn chr1 161966935 162084477 - 0
+NM_178051_Mterfd2 chr1 95195779 95202630 - 0
+NM_178055_Dnajb2 chr1 75233016 75242264 + 0
+NM_178119_Agap1 chr1 91351421 91791845 + 0
+NM_178241_Il8ra chr1 74238380 74241205 - 0
+NM_178243_5830403L16Rik chr1 155697272 155747352 - 0
+NM_178244_Teddm1 chr1 155724147 155740188 + 0
+NM_178399_3110035E14Rik chr1 9591248 9617222 + 0
+NM_178405_Atp1a2 chr1 174201852 174233438 - 0
+NM_178593_Rcsd1 chr1 167572007 167639868 - 0
+NM_178598_Tagln2 chr1 174430123 174475991 + 0
+NM_178601_Imp4 chr1 34496377 34511555 + 0
+NM_178632_Ints7 chr1 193399085 193447550 + 0
+NM_178653_Sccpdh chr1 181598088 181617593 + 0
+NM_178690_Rab3gap1 chr1 129765355 129840723 + 0
+NM_178691_Yod1 chr1 132612680 132618643 + 0
+NM_178692_C130074G19Rik chr1 186695805 186707077 - 0
+NM_178775_Rps6kc1 chr1 192524091 192736016 - 0
+NM_178779_Rnf152 chr1 107176426 107253513 - 0
+NM_178874_Tmcc2 chr1 134252895 134288369 - 0
+NM_178883_Gorab chr1 165315039 165340946 - 0
+NM_178884_Obsl1 chr1 75482401 75503218 - 0
+NM_181405_Rnpepl1 chr1 94807467 94817954 + 0
+NM_181546_Syt14 chr1 194713536 194861959 - 0
+NM_181750_R3hdm1 chr1 129999892 130134312 + 0
+NM_181796_Gstp2 chr1 193897651 193905509 - 0
+NM_182716_Nfasc chr1 134445291 134638354 - 0
+NM_182930_Plekha6 chr1 135077806 135200008 + 0
+NM_183019_Arhgef4 chr1 34788954 34873560 + 0
+NM_183022_Accn4 chr1 75447063 75470207 + 0
+NM_183027_Ap1s3 chr1 79591820 79668545 - 0
+NM_183028_Pcmtd1 chr1 7079053 7163709 + 0
+NM_183124_Defb41 chr1 18241071 18350659 - 0
+NM_183355_Pbx1 chr1 170049495 170512777 - 0
+NM_183391_Tnfsf18 chr1 163373523 163524094 + 0
+NM_194333_Slc23a3 chr1 75120731 75130464 - 0
+NM_198006_6330578E17Rik chr1 37473934 37474944 - 0
+NM_198006_6330578E17Rik chr1 37477057 37486928 - 0
+NM_198028_Serpinb10 chr1 109425580 109445838 + 0
+NM_198127_Abi2 chr1 60466022 60537998 + 0
+NM_198247_Sertad4 chr1 194670313 194693726 - 0
+NM_198303_Eif5b chr1 38054627 38112414 + 0
+NM_198652_6430706D22Rik chr1 90158880 90174174 - 0
+NM_198653_Iars2 chr1 187109458 187153280 - 0
+NM_198654_Nsl1 chr1 192886918 192919389 + 0
+NM_198680_Serpinb3b chr1 109033488 109059720 - 0
+NM_198899_Ugcgl1 chr1 36196873 36301555 - 0
+NM_198934_Pou2f1 chr1 167804181 167932753 - 0
+NM_199007_Sgol2 chr1 58026657 58085164 + 0
+NM_199021_Dpp10 chr1 125044486 126749525 - 0
+NM_201363_Serpinb3c chr1 109088051 109198931 - 0
+NM_201376_Serpinb3d chr1 108974770 108980057 - 0
+NM_201641_Ugt1a10 chr1 89922380 90115570 + 0
+NM_206896_Olfr12 chr1 94516341 94538591 + 0
+NM_207031_Ano7 chr1 95270385 95302271 + 0
+NM_207137_Olfr417 chr1 176299050 176299979 + 0
+NM_207137_Olfr417 chr1 176321202 176322113 + 0
+NM_207158_Olfr427 chr1 176028781 176030538 + 0
+NM_207225_Hdac4 chr1 93755950 94103099 - 0
+NM_207228_Tsga10 chr1 37783457 37922148 - 0
+NM_207233_C1ql2 chr1 122196386 122239751 + 0
+NM_207281_4832428D23Rik chr1 44260915 44515719 - 0
+NM_207583_Fam5b chr1 160175402 160286644 - 0
+NM_207653_Cflar chr1 58768296 58813658 + 0
+NM_207653_Cflar chr1 58813703 58815725 + 0
+NM_213616_Atp2b4 chr1 135602265 135697538 - 0
+NR_002840_Gas5 chr1 162964758 162968663 + 0
+NR_002858_EG241041 chr1 21268965 21306401 - 0
+NR_002870_Dnm3os chr1 164119785 164155671 + 0
+NR_003623_EG277333 chr1 182251970 182262902 - 0
+NR_026896_4931440L10Rik chr1 136437533 136449760 - 0
diff -r 000000000000 -r 0abe6bac47a6 test-data/features_per_peak1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_per_peak1.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,70 @@
+#peak.chr peak.start peak.end gene.id_1 strand_1 TSS_1 TES_1 dist_closest_1 dist_TSS_1 dist_TES_1 direction_1 overlap_gene_1 overlap_promoter_1 gene.id_2 strand_2 TSS_2 TES_2 dist_closest_2 dist_TSS_2 dist_TES_2 direction_2 overlap_gene_2 overlap_promoter_2 gene.id_3 strand_3 TSS_3 TES_3 dist_closest_3 dist_TSS_3 dist_TES_3 direction_3 overlap_gene_3 overlap_promoter_3 gene.id_4 strand_4 TSS_4 TES_4 dist_closest_4 dist_TSS_4 dist_TES_4 direction_4 overlap_gene_4 overlap_promoter_4
+chr1 10617233 10617437 NM_177834_Cpa6 - 10710026 10314801 0 92589 302432 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 108747519 108747791 NM_009190_Vps4b - 108739123 108665873 8396 8396 81646 U 0 1 NM_009257_Serpinb5 + 108757652 108779925 9861 9861 32134 U 0 1 NM_027971_Serpinb12 + 108831026 108853655 83235 83235 105864 U 0 0 NM_027534_Kdsr - 108656357 108617007 91162 91162 130512 U 0 0
+chr1 120760212 120760461 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 132950929 132951247 NM_010548_Il10 + 132916424 132921547 29382 34505 29382 D 0 0 NM_001009940_Il19 - 132915234 132786042 35695 35695 164887 U 0 0 NM_008551_Mapkapk2 - 133013820 132950274 0 62573 655 . 1 0 NM_145508_Dyrk3 - 133034897 133018921 67674 83650 67674 D 0 0
+chr1 133114860 133115015 NM_018750_Rassf5 - 133144761 133072991 0 29746 41869 . 1 0 NM_019777_Ikbke - 133176163 133151052 36037 61148 36037 D 0 0 NM_001136070_Lgtn + 133049773 133084235 30625 65087 30625 D 0 0 NM_145508_Dyrk3 - 133034897 133018921 79963 79963 95939 U 0 0
+chr1 135582677 135582828 NM_001159649_Lax1 - 135586665 135575626 0 3837 7051 . 1 0 NM_144530_Zc3h11a - 135557956 135516445 24721 24721 66232 U 0 0 NM_213616_Atp2b4 - 135697538 135602265 19437 114710 19437 D 0 0 . . . . . . . . . .
+chr1 135851853 135852218 NM_054077_Prelp - 135865173 135806855 0 12955 44998 . 1 0 NM_054076_Optc - 135805299 135787973 46554 46554 63880 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 136956468 136956598 NM_007955_Ptprv - 137029151 137004306 47708 72553 47708 D 0 0 NM_026823_Arl8a + 137043216 137053347 86618 86618 96749 U 0 0 NM_026024_Ube2t + 136857731 136870739 85729 98737 85729 D 0 0 NM_134438_Gpr37l1 - 137069087 137054243 97645 112489 97645 D 0 0
+chr1 13829227 13829564 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 138437726 138437860 NM_177643_Zfp281 + 138487073 138526617 49213 49213 88757 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 140381656 140381785 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 145591041 145591176 NM_001038592_Glrx2 + 145585774 145608282 0 5267 17106 . 1 0 NM_019562_Uchl5 + 145623774 145654586 32598 32598 63410 U 0 0 NM_013835_Trove2 - 145624178 145597816 6640 33002 6640 D 0 0 NM_145991_Cdc73 - 145549936 145274292 41105 41105 316749 U 0 0
+chr1 154971572 154971673 NM_008485_Lamc2 - 155033557 154969890 0 61884 1682 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 155123313 155123435 NM_010683_Lamc1 - 155179906 155065803 0 56471 57510 . 1 0 NM_008485_Lamc2 - 155033557 154969890 89756 89756 153423 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 158510523 158510813 NM_009230_Soat1 - 158417632 158354679 92891 92891 155844 U 0 0 NM_023141_Tor3a - 158604477 158583760 72947 93664 72947 D 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 158537267 158537411 NM_023141_Tor3a - 158604477 158583760 46349 67066 46349 D 0 0 NM_145413_Fam20b - 158649180 158608676 71265 111769 71265 D 0 0 NM_009230_Soat1 - 158417632 158354679 119635 119635 182588 U 0 0 . . . . . . . . . .
+chr1 158580638 158580759 NM_023141_Tor3a - 158604477 158583760 3001 23718 3001 D 0 0 NM_145413_Fam20b - 158649180 158608676 27917 68421 27917 D 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 158835251 158835391 NM_028333_Angptl1 + 158769061 158791209 44042 66190 44042 D 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 163827897 163828062 NM_026078_Pigc + 163860747 163957217 32685 32685 129155 U 0 0 NM_010177_Fasl - 163718844 163710820 109053 109053 117077 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 164215623 164215935 NR_002870_Dnm3os + 164119785 164155671 59952 95838 59952 D 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 167222964 167223261 NM_145513_Tiprl - 167183116 167133855 39848 39848 89109 U 0 0 NM_145512_Sft2d2 - 167124549 167104119 98415 98415 118845 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 167906284 167906554 NM_198934_Pou2f1 - 167932753 167804181 0 26199 102103 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 170255081 170255260 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 17030405 17030545 NM_020604_Jph1 - 17087942 16837549 0 57397 192856 . 1 0 NM_010267_Gdap1 + 17135463 17385513 104918 104918 354968 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 172620779 172620912 NM_177068_Olfml2b + 172569075 172612915 7864 51704 7864 D 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 172620917 172621080 NM_177068_Olfml2b + 172569075 172612915 8002 51842 8002 D 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 174376470 174376659 NM_029612_Slamf9 + 174392516 174408706 15857 15857 32047 U 0 0 NM_033608_Igsf9 + 174411686 174429005 35027 35027 52346 U 0 0 NM_178598_Tagln2 + 174430123 174475991 53464 53464 99332 U 0 0 NM_026234_Pigm + 174306609 174314210 62260 69861 62260 D 0 0
+chr1 181061299 181061446 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 182479646 182479905 NM_007415_Parp1 + 182499033 182531385 19128 19128 51480 U 0 0 NM_001103182_Lin9 + 182572002 182620816 92097 92097 140911 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 185854947 185855105 NM_022019_Dusp10 + 185755009 185899515 0 99938 44410 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 194258648 194259032 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 194645118 194645475 NM_144881_Hhat - 194649833 194320603 0 4358 324515 . 1 0 ENSMUST00000057543_A730013G03Rik - 194661397 194659323 13848 15922 13848 D 0 0 NM_198247_Sertad4 - 194693726 194670313 24838 48251 24838 D 0 0 . . . . . . . . . .
+chr1 194957396 194957723 NM_145415_AA408296 - 194956446 194918802 950 950 38594 U 0 1 NM_016851_Irf6 + 194979326 194998230 21603 21603 40507 U 0 0 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 U 0 0 NM_153137_Traf3ip3 - 195027877 195001656 43933 70154 43933 D 0 0
+chr1 195324443 195324741 NM_144817_Camk1g - 195216632 195172540 107811 107811 151903 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195330701 195330930 NM_144817_Camk1g - 195216632 195172540 114069 114069 158161 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195338316 195338616 NM_144817_Camk1g - 195216632 195172540 121684 121684 165776 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195342728 195342985 NM_144817_Camk1g - 195216632 195172540 126096 126096 170188 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195384767 195385195 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 197057796 197057843 NM_007758_Cr2 - 197003002 196963005 54794 54794 94791 U 0 0 NM_013499_Cr1l - 196957754 196924298 100042 100042 133498 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 24609562 24609623 NM_007733_Col19a1 - 24602262 24258667 7300 7300 350895 U 0 1 NM_026719_Lmbrd1 + 24593456 24847969 0 16106 238346 . 1 0 . . . . . . . . . . . . . . . . . . . .
+chr1 24609923 24609992 NM_007733_Col19a1 - 24602262 24258667 7661 7661 351256 U 0 1 NM_026719_Lmbrd1 + 24593456 24847969 0 16467 237977 . 1 0 . . . . . . . . . . . . . . . . . . . .
+chr1 24730996 24731077 NM_026719_Lmbrd1 + 24820582 24823143 89505 89505 92066 U 0 0 NM_007733_Col19a1 - 24602262 24258667 128734 128734 472329 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 26734195 26734485 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 34206924 34207100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 36106813 36107058 NM_015818_Hs6st1 + 36125255 36163289 18197 18197 56231 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 39492140 39492513 NM_018775_Tbc1d8 - 39544345 39428350 0 51832 63790 . 1 0 NM_053257_Rpl31 + 39421000 39429094 63046 71140 63046 D 0 0 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 U 0 0 . . . . . . . . . .
+chr1 40325917 40326123 NM_008362_Il1r1 + 40274145 40373439 0 51772 47316 . 1 0 NM_133193_Il1rl2 + 40381454 40447345 55331 55331 121222 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 44195449 44195639 NM_011729_Ercc5 + 44204270 44256568 8631 8631 60929 U 0 1 NM_023645_Kdelc1 - 44177102 44143458 18347 18347 51991 U 0 0 NM_144558_Bivm + 44175822 44201615 0 19627 5976 . 1 0 . . . . . . . . . .
+chr1 52625416 52625560 NM_008667_Nab1 - 52611216 52487127 14200 14200 138289 U 0 0 NM_001142647_Tmem194b + 52687569 52708760 62009 62009 83200 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 54631692 54631815 ENSMUST00000094950_Pgap1 - 54614539 54529849 17153 17153 101843 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 55283572 55283675 NM_028713_Rftn2 - 55283748 55227030 0 73 56542 . 1 1 NM_175439_Mars2 + 55294084 55297625 10409 10409 13950 U 0 0 NM_025283_Mobkl3 + 55187734 55211736 71836 95838 71836 D 0 0 . . . . . . . . . .
+chr1 63664888 63665018 NM_011780_Adam23 + 63640970 63642850 22038 23918 22038 D 0 0 NM_029696_Mdh1b - 63776894 63745401 80383 111876 80383 D 0 0 NM_172422_Fastkd2 + 63777134 63803028 112116 112116 138010 U 0 0 . . . . . . . . . .
+chr1 72769824 72770056 NM_176980_Ankar - 72747143 72689581 22681 22681 80243 U 0 0 NM_008342_Igfbp2 + 72840313 72899038 70257 70257 128982 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 72770058 72770226 NM_176980_Ankar - 72747143 72689581 22915 22915 80477 U 0 0 NM_008342_Igfbp2 + 72840313 72899038 70087 70087 128812 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 72815517 72815742 NM_008342_Igfbp2 + 72840313 72899038 24571 24571 83296 U 0 0 NM_176980_Ankar - 72747143 72689581 68374 68374 125936 U 0 0 NM_010518_Igfbp5 - 72921468 72904507 88765 105726 88765 D 0 0 . . . . . . . . . .
+chr1 75481920 75482054 NM_001001565_Chpf - 75476437 75470923 5483 5483 10997 U 0 1 NM_178884_Obsl1 - 75503218 75482401 347 21164 347 D 0 0 NM_010564_Inha + 75503647 75506924 21593 21593 24870 U 0 0 NM_183022_Accn4 + 75447063 75470207 11713 34857 11713 D 0 0
+chr1 77457642 77457791 NM_007936_Epha4 - 77511653 77280640 0 53862 177002 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 78630893 78631160 NM_028817_Acsl3 + 78654388 78743434 23228 23228 112274 U 0 0 NM_011811_Farsb - 78506689 78414533 124204 124204 216360 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 88408969 88409267 NM_172974_Cops7b + 88478926 88503950 69659 69659 94683 U 0 0 NM_008801_Pde6d - 88479102 88427331 18064 69835 18064 D 0 0 NM_010341_Nmur1 - 88297441 88282479 111528 111528 126490 U 0 0 . . . . . . . . . .
+chr1 89989553 89989714 NM_201641_Ugt1a10 + 89922380 90115570 0 67173 125856 . 1 0 NM_008299_Dnajb3 - 90102337 90101307 111593 112623 111593 D 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 90412932 90413132 NM_008132_Glrp1 - 90406631 90396446 6301 6301 16486 U 0 1 NM_029269_Spp2 + 90303568 90373213 39719 109364 39719 D 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 90592499 90592629 NM_177305_Arl4c - 90617572 90569702 0 24943 22797 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 91496003 91496145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 91496155 91496319 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 92070253 92070431 NM_007722_Cxcr7 + 92100063 92112863 29632 29632 42432 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 95186508 95186637 NM_178051_Mterfd2 - 95202630 95195779 9142 15993 9142 D 0 0 NM_023200_Ppp1r7 + 95239431 95266345 52794 52794 79708 U 0 0 NM_080850_Pask - 95240039 95205357 18720 53402 18720 D 0 0 NM_172463_Sned1 + 95132418 95197642 0 54090 11005 . 1 0
+chr1 9619046 9619167 NM_178399_3110035E14Rik + 9591248 9617222 1824 27798 1824 D 0 0 NM_008651_Mybl1 - 9690280 9635825 16658 71113 16658 D 0 0 NM_175236_Adhfe1 + 9538049 9570746 48300 80997 48300 D 0 0 NM_021511_Rrs1 + 9535513 9537532 81514 83533 81514 D 0 0
+chr1 9619175 9619382 NM_178399_3110035E14Rik + 9591248 9617222 1953 27927 1953 D 0 0 NM_008651_Mybl1 - 9690280 9635825 16443 70898 16443 D 0 0 NM_175236_Adhfe1 + 9538049 9570746 48429 81126 48429 D 0 0 NM_021511_Rrs1 + 9535513 9537532 81643 83662 81643 D 0 0
diff -r 000000000000 -r 0abe6bac47a6 test-data/features_per_peak2.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_per_peak2.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,140 @@
+#peak.chr peak.start peak.end gene.id strand TSS TES dist_closest dist_TSS dist_TES direction overlap_gene overlap_promoter
+chr1 10617233 10617437 NM_177834_Cpa6 - 10710026 10314801 0 92589 302432 . 1 0
+chr1 108747519 108747791 NM_009190_Vps4b - 108739123 108665873 8396 8396 81646 U 0 0
+chr1 108747519 108747791 NM_009257_Serpinb5 + 108757652 108779925 9861 9861 32134 U 0 0
+chr1 108747519 108747791 NM_027971_Serpinb12 + 108831026 108853655 83235 83235 105864 U 0 0
+chr1 108747519 108747791 NM_027534_Kdsr - 108656357 108617007 91162 91162 130512 U 0 0
+chr1 120760212 120760461 --- --- --- --- --- --- --- --- --- ---
+chr1 132950929 132951247 NM_010548_Il10 + 132916424 132921547 29382 34505 29382 D 0 0
+chr1 132950929 132951247 NM_001009940_Il19 - 132915234 132786042 35695 35695 164887 U 0 0
+chr1 132950929 132951247 NM_008551_Mapkapk2 - 133013820 132950274 0 62573 655 . 1 0
+chr1 132950929 132951247 NM_145508_Dyrk3 - 133034897 133018921 67674 83650 67674 D 0 0
+chr1 133114860 133115015 NM_018750_Rassf5 - 133144761 133072991 0 29746 41869 . 1 0
+chr1 133114860 133115015 NM_019777_Ikbke - 133176163 133151052 36037 61148 36037 D 0 0
+chr1 133114860 133115015 NM_001136070_Lgtn + 133049773 133084235 30625 65087 30625 D 0 0
+chr1 133114860 133115015 NM_145508_Dyrk3 - 133034897 133018921 79963 79963 95939 U 0 0
+chr1 135582677 135582828 NM_001159649_Lax1 - 135586665 135575626 0 3837 7051 . 1 0
+chr1 135582677 135582828 NM_144530_Zc3h11a - 135557956 135516445 24721 24721 66232 U 0 0
+chr1 135582677 135582828 NM_213616_Atp2b4 - 135697538 135602265 19437 114710 19437 D 0 0
+chr1 135851853 135852218 NM_054077_Prelp - 135865173 135806855 0 12955 44998 . 1 0
+chr1 135851853 135852218 NM_054076_Optc - 135805299 135787973 46554 46554 63880 U 0 0
+chr1 136956468 136956598 NM_007955_Ptprv - 137029151 137004306 47708 72553 47708 D 0 0
+chr1 136956468 136956598 NM_026823_Arl8a + 137043216 137053347 86618 86618 96749 U 0 0
+chr1 136956468 136956598 NM_026024_Ube2t + 136857731 136870739 85729 98737 85729 D 0 0
+chr1 136956468 136956598 NM_134438_Gpr37l1 - 137069087 137054243 97645 112489 97645 D 0 0
+chr1 13829227 13829564 --- --- --- --- --- --- --- --- --- ---
+chr1 138437726 138437860 NM_177643_Zfp281 + 138487073 138526617 49213 49213 88757 U 0 0
+chr1 140381656 140381785 --- --- --- --- --- --- --- --- --- ---
+chr1 145591041 145591176 NM_001038592_Glrx2 + 145585774 145608282 0 5267 17106 . 1 0
+chr1 145591041 145591176 NM_019562_Uchl5 + 145623774 145654586 32598 32598 63410 U 0 0
+chr1 145591041 145591176 NM_013835_Trove2 - 145624178 145597816 6640 33002 6640 D 0 0
+chr1 145591041 145591176 NM_145991_Cdc73 - 145549936 145274292 41105 41105 316749 U 0 0
+chr1 154971572 154971673 NM_008485_Lamc2 - 155033557 154969890 0 61884 1682 . 1 0
+chr1 155123313 155123435 NM_010683_Lamc1 - 155179906 155065803 0 56471 57510 . 1 0
+chr1 155123313 155123435 NM_008485_Lamc2 - 155033557 154969890 89756 89756 153423 U 0 0
+chr1 158510523 158510813 NM_009230_Soat1 - 158417632 158354679 92891 92891 155844 U 0 0
+chr1 158510523 158510813 NM_023141_Tor3a - 158604477 158583760 72947 93664 72947 D 0 0
+chr1 158537267 158537411 NM_023141_Tor3a - 158604477 158583760 46349 67066 46349 D 0 0
+chr1 158537267 158537411 NM_145413_Fam20b - 158649180 158608676 71265 111769 71265 D 0 0
+chr1 158537267 158537411 NM_009230_Soat1 - 158417632 158354679 119635 119635 182588 U 0 0
+chr1 158580638 158580759 NM_023141_Tor3a - 158604477 158583760 3001 23718 3001 D 0 0
+chr1 158580638 158580759 NM_145413_Fam20b - 158649180 158608676 27917 68421 27917 D 0 0
+chr1 158835251 158835391 NM_028333_Angptl1 + 158769061 158791209 44042 66190 44042 D 0 0
+chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 U 0 0
+chr1 163827897 163828062 NM_026078_Pigc + 163860747 163957217 32685 32685 129155 U 0 0
+chr1 163827897 163828062 NM_010177_Fasl - 163718844 163710820 109053 109053 117077 U 0 0
+chr1 164215623 164215935 NR_002870_Dnm3os + 164119785 164155671 59952 95838 59952 D 0 0
+chr1 167222964 167223261 NM_145513_Tiprl - 167183116 167133855 39848 39848 89109 U 0 0
+chr1 167222964 167223261 NM_145512_Sft2d2 - 167124549 167104119 98415 98415 118845 U 0 0
+chr1 167906284 167906554 NM_198934_Pou2f1 - 167932753 167804181 0 26199 102103 . 1 0
+chr1 170255081 170255260 --- --- --- --- --- --- --- --- --- ---
+chr1 17030405 17030545 NM_020604_Jph1 - 17087942 16837549 0 57397 192856 . 1 0
+chr1 17030405 17030545 NM_010267_Gdap1 + 17135463 17385513 104918 104918 354968 U 0 0
+chr1 172620779 172620912 NM_177068_Olfml2b + 172569075 172612915 7864 51704 7864 D 0 0
+chr1 172620917 172621080 NM_177068_Olfml2b + 172569075 172612915 8002 51842 8002 D 0 0
+chr1 174376470 174376659 NM_029612_Slamf9 + 174392516 174408706 15857 15857 32047 U 0 0
+chr1 174376470 174376659 NM_033608_Igsf9 + 174411686 174429005 35027 35027 52346 U 0 0
+chr1 174376470 174376659 NM_178598_Tagln2 + 174430123 174475991 53464 53464 99332 U 0 0
+chr1 174376470 174376659 NM_026234_Pigm + 174306609 174314210 62260 69861 62260 D 0 0
+chr1 181061299 181061446 --- --- --- --- --- --- --- --- --- ---
+chr1 182479646 182479905 NM_007415_Parp1 + 182499033 182531385 19128 19128 51480 U 0 0
+chr1 182479646 182479905 NM_001103182_Lin9 + 182572002 182620816 92097 92097 140911 U 0 0
+chr1 185854947 185855105 NM_022019_Dusp10 + 185755009 185899515 0 99938 44410 . 1 0
+chr1 194258648 194259032 --- --- --- --- --- --- --- --- --- ---
+chr1 194645118 194645475 NM_144881_Hhat - 194649833 194320603 0 4358 324515 . 1 0
+chr1 194645118 194645475 ENSMUST00000057543_A730013G03Rik - 194661397 194659323 13848 15922 13848 D 0 0
+chr1 194645118 194645475 NM_198247_Sertad4 - 194693726 194670313 24838 48251 24838 D 0 0
+chr1 194957396 194957723 NM_145415_AA408296 - 194956446 194918802 950 950 38594 U 0 1
+chr1 194957396 194957723 NM_016851_Irf6 + 194979326 194998230 21603 21603 40507 U 0 0
+chr1 194957396 194957723 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 U 0 0
+chr1 194957396 194957723 NM_153137_Traf3ip3 - 195027877 195001656 43933 70154 43933 D 0 0
+chr1 195324443 195324741 NM_144817_Camk1g - 195216632 195172540 107811 107811 151903 U 0 0
+chr1 195330701 195330930 NM_144817_Camk1g - 195216632 195172540 114069 114069 158161 U 0 0
+chr1 195338316 195338616 NM_144817_Camk1g - 195216632 195172540 121684 121684 165776 U 0 0
+chr1 195342728 195342985 NM_144817_Camk1g - 195216632 195172540 126096 126096 170188 U 0 0
+chr1 195384767 195385195 --- --- --- --- --- --- --- --- --- ---
+chr1 197057796 197057843 NM_007758_Cr2 - 197003002 196963005 54794 54794 94791 U 0 0
+chr1 197057796 197057843 NM_013499_Cr1l - 196957754 196924298 100042 100042 133498 U 0 0
+chr1 24609562 24609623 NM_007733_Col19a1 - 24602262 24258667 7300 7300 350895 U 0 0
+chr1 24609562 24609623 NM_026719_Lmbrd1 + 24593456 24847969 0 16106 238346 . 1 0
+chr1 24609923 24609992 NM_007733_Col19a1 - 24602262 24258667 7661 7661 351256 U 0 0
+chr1 24609923 24609992 NM_026719_Lmbrd1 + 24593456 24847969 0 16467 237977 . 1 0
+chr1 24730996 24731077 NM_026719_Lmbrd1 + 24820582 24823143 89505 89505 92066 U 0 0
+chr1 24730996 24731077 NM_007733_Col19a1 - 24602262 24258667 128734 128734 472329 U 0 0
+chr1 26734195 26734485 --- --- --- --- --- --- --- --- --- ---
+chr1 34206924 34207100 --- --- --- --- --- --- --- --- --- ---
+chr1 36106813 36107058 NM_015818_Hs6st1 + 36125255 36163289 18197 18197 56231 U 0 0
+chr1 39492140 39492513 NM_018775_Tbc1d8 - 39544345 39428350 0 51832 63790 . 1 0
+chr1 39492140 39492513 NM_053257_Rpl31 + 39421000 39429094 63046 71140 63046 D 0 0
+chr1 39492140 39492513 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 U 0 0
+chr1 40325917 40326123 NM_008362_Il1r1 + 40274145 40373439 0 51772 47316 . 1 0
+chr1 40325917 40326123 NM_133193_Il1rl2 + 40381454 40447345 55331 55331 121222 U 0 0
+chr1 44195449 44195639 NM_011729_Ercc5 + 44204270 44256568 8631 8631 60929 U 0 0
+chr1 44195449 44195639 NM_023645_Kdelc1 - 44177102 44143458 18347 18347 51991 U 0 0
+chr1 44195449 44195639 NM_144558_Bivm + 44175822 44201615 0 19627 5976 . 1 0
+chr1 52625416 52625560 NM_008667_Nab1 - 52611216 52487127 14200 14200 138289 U 0 0
+chr1 52625416 52625560 NM_001142647_Tmem194b + 52687569 52708760 62009 62009 83200 U 0 0
+chr1 54631692 54631815 ENSMUST00000094950_Pgap1 - 54614539 54529849 17153 17153 101843 U 0 0
+chr1 55283572 55283675 NM_028713_Rftn2 - 55283748 55227030 0 73 56542 . 1 1
+chr1 55283572 55283675 NM_175439_Mars2 + 55294084 55297625 10409 10409 13950 U 0 0
+chr1 55283572 55283675 NM_025283_Mobkl3 + 55187734 55211736 71836 95838 71836 D 0 0
+chr1 63664888 63665018 NM_011780_Adam23 + 63640970 63642850 22038 23918 22038 D 0 0
+chr1 63664888 63665018 NM_029696_Mdh1b - 63776894 63745401 80383 111876 80383 D 0 0
+chr1 63664888 63665018 NM_172422_Fastkd2 + 63777134 63803028 112116 112116 138010 U 0 0
+chr1 72769824 72770056 NM_176980_Ankar - 72747143 72689581 22681 22681 80243 U 0 0
+chr1 72769824 72770056 NM_008342_Igfbp2 + 72840313 72899038 70257 70257 128982 U 0 0
+chr1 72770058 72770226 NM_176980_Ankar - 72747143 72689581 22915 22915 80477 U 0 0
+chr1 72770058 72770226 NM_008342_Igfbp2 + 72840313 72899038 70087 70087 128812 U 0 0
+chr1 72815517 72815742 NM_008342_Igfbp2 + 72840313 72899038 24571 24571 83296 U 0 0
+chr1 72815517 72815742 NM_176980_Ankar - 72747143 72689581 68374 68374 125936 U 0 0
+chr1 72815517 72815742 NM_010518_Igfbp5 - 72921468 72904507 88765 105726 88765 D 0 0
+chr1 75481920 75482054 NM_001001565_Chpf - 75476437 75470923 5483 5483 10997 U 0 0
+chr1 75481920 75482054 NM_178884_Obsl1 - 75503218 75482401 347 21164 347 D 0 0
+chr1 75481920 75482054 NM_010564_Inha + 75503647 75506924 21593 21593 24870 U 0 0
+chr1 75481920 75482054 NM_183022_Accn4 + 75447063 75470207 11713 34857 11713 D 0 0
+chr1 77457642 77457791 NM_007936_Epha4 - 77511653 77280640 0 53862 177002 . 1 0
+chr1 78630893 78631160 NM_028817_Acsl3 + 78654388 78743434 23228 23228 112274 U 0 0
+chr1 78630893 78631160 NM_011811_Farsb - 78506689 78414533 124204 124204 216360 U 0 0
+chr1 88408969 88409267 NM_172974_Cops7b + 88478926 88503950 69659 69659 94683 U 0 0
+chr1 88408969 88409267 NM_008801_Pde6d - 88479102 88427331 18064 69835 18064 D 0 0
+chr1 88408969 88409267 NM_010341_Nmur1 - 88297441 88282479 111528 111528 126490 U 0 0
+chr1 89989553 89989714 NM_201641_Ugt1a10 + 89922380 90115570 0 67173 125856 . 1 0
+chr1 89989553 89989714 NM_008299_Dnajb3 - 90102337 90101307 111593 112623 111593 D 0 0
+chr1 90412932 90413132 NM_008132_Glrp1 - 90406631 90396446 6301 6301 16486 U 0 0
+chr1 90412932 90413132 NM_029269_Spp2 + 90303568 90373213 39719 109364 39719 D 0 0
+chr1 90592499 90592629 NM_177305_Arl4c - 90617572 90569702 0 24943 22797 . 1 0
+chr1 91496003 91496145 --- --- --- --- --- --- --- --- --- ---
+chr1 91496155 91496319 --- --- --- --- --- --- --- --- --- ---
+chr1 92070253 92070431 NM_007722_Cxcr7 + 92100063 92112863 29632 29632 42432 U 0 0
+chr1 95186508 95186637 NM_178051_Mterfd2 - 95202630 95195779 9142 15993 9142 D 0 0
+chr1 95186508 95186637 NM_023200_Ppp1r7 + 95239431 95266345 52794 52794 79708 U 0 0
+chr1 95186508 95186637 NM_080850_Pask - 95240039 95205357 18720 53402 18720 D 0 0
+chr1 95186508 95186637 NM_172463_Sned1 + 95132418 95197642 0 54090 11005 . 1 0
+chr1 9619046 9619167 NM_178399_3110035E14Rik + 9591248 9617222 1824 27798 1824 D 0 0
+chr1 9619046 9619167 NM_008651_Mybl1 - 9690280 9635825 16658 71113 16658 D 0 0
+chr1 9619046 9619167 NM_175236_Adhfe1 + 9538049 9570746 48300 80997 48300 D 0 0
+chr1 9619046 9619167 NM_021511_Rrs1 + 9535513 9537532 81514 83533 81514 D 0 0
+chr1 9619175 9619382 NM_178399_3110035E14Rik + 9591248 9617222 1953 27927 1953 D 0 0
+chr1 9619175 9619382 NM_008651_Mybl1 - 9690280 9635825 16443 70898 16443 D 0 0
+chr1 9619175 9619382 NM_175236_Adhfe1 + 9538049 9570746 48429 81126 48429 D 0 0
+chr1 9619175 9619382 NM_021511_Rrs1 + 9535513 9537532 81643 83662 81643 D 0 0
diff -r 000000000000 -r 0abe6bac47a6 test-data/features_per_peak3.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_per_peak3.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,70 @@
+#peak.chr peak.start peak.end gene.id_1 strand_1 TSS_1 TES_1 dist_closest_1 dist_TSS_1 dist_TES_1 direction_1 overlap_gene_1 overlap_promoter_1 gene.id_2 strand_2 TSS_2 TES_2 dist_closest_2 dist_TSS_2 dist_TES_2 direction_2 overlap_gene_2 overlap_promoter_2 gene.id_3 strand_3 TSS_3 TES_3 dist_closest_3 dist_TSS_3 dist_TES_3 direction_3 overlap_gene_3 overlap_promoter_3 gene.id_4 strand_4 TSS_4 TES_4 dist_closest_4 dist_TSS_4 dist_TES_4 direction_4 overlap_gene_4 overlap_promoter_4
+chr1 10617233 10617437 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 108747519 108747791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 120760212 120760461 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 132950929 132951247 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 133114860 133115015 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 135582677 135582828 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 135851853 135852218 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 136956468 136956598 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 13829227 13829564 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 138437726 138437860 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 140381656 140381785 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 145591041 145591176 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 154971572 154971673 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 155123313 155123435 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 158510523 158510813 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 158537267 158537411 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 158580638 158580759 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 158835251 158835391 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 163827897 163828062 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 164215623 164215935 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 167222964 167223261 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 167906284 167906554 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 170255081 170255260 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 17030405 17030545 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 172620779 172620912 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 172620917 172621080 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 174376470 174376659 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 181061299 181061446 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 182479646 182479905 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 185854947 185855105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 194258648 194259032 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 194645118 194645475 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 194957396 194957723 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195324443 195324741 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195330701 195330930 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195338316 195338616 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195342728 195342985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195384767 195385195 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 197057796 197057843 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 24609562 24609623 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 24609923 24609992 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 24730996 24731077 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 26734195 26734485 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 34206924 34207100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 36106813 36107058 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 39492140 39492513 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 40325917 40326123 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 44195449 44195639 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 52625416 52625560 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 54631692 54631815 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 55283572 55283675 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 63664888 63665018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 72769824 72770056 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 72770058 72770226 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 72815517 72815742 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 75481920 75482054 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 77457642 77457791 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 78630893 78631160 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 88408969 88409267 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 89989553 89989714 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 90412932 90413132 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 90592499 90592629 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 91496003 91496145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 91496155 91496319 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 92070253 92070431 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 95186508 95186637 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 9619046 9619167 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 9619175 9619382 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
diff -r 000000000000 -r 0abe6bac47a6 test-data/features_per_peak4.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_per_peak4.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,277 @@
+#peak.chr peak.start peak.end gene.id strand TSS TES dist_closest dist_TSS dist_TES direction overlap_gene overlap_promoter
+chr1 10617233 10617437 NM_177834_Cpa6 - 10710026 10314801 0 92589 302432 . 1 0
+chr1 10617233 10617437 --- --- --- --- --- --- --- --- --- ---
+chr1 10617233 10617437 --- --- --- --- --- --- --- --- --- ---
+chr1 10617233 10617437 --- --- --- --- --- --- --- --- --- ---
+chr1 108747519 108747791 NM_009190_Vps4b - 108739123 108665873 8396 8396 81646 U 0 0
+chr1 108747519 108747791 NM_009257_Serpinb5 + 108757652 108779925 9861 9861 32134 U 0 0
+chr1 108747519 108747791 NM_027971_Serpinb12 + 108831026 108853655 83235 83235 105864 U 0 0
+chr1 108747519 108747791 NM_027534_Kdsr - 108656357 108617007 91162 91162 130512 U 0 0
+chr1 120760212 120760461 --- --- --- --- --- --- --- --- --- ---
+chr1 120760212 120760461 --- --- --- --- --- --- --- --- --- ---
+chr1 120760212 120760461 --- --- --- --- --- --- --- --- --- ---
+chr1 120760212 120760461 --- --- --- --- --- --- --- --- --- ---
+chr1 132950929 132951247 NM_010548_Il10 + 132916424 132921547 29382 34505 29382 D 0 0
+chr1 132950929 132951247 NM_001009940_Il19 - 132915234 132786042 35695 35695 164887 U 0 0
+chr1 132950929 132951247 NM_008551_Mapkapk2 - 133013820 132950274 0 62573 655 . 1 0
+chr1 132950929 132951247 NM_145508_Dyrk3 - 133034897 133018921 67674 83650 67674 D 0 0
+chr1 133114860 133115015 NM_018750_Rassf5 - 133144761 133072991 0 29746 41869 . 1 0
+chr1 133114860 133115015 NM_019777_Ikbke - 133176163 133151052 36037 61148 36037 D 0 0
+chr1 133114860 133115015 NM_001136070_Lgtn + 133049773 133084235 30625 65087 30625 D 0 0
+chr1 133114860 133115015 NM_145508_Dyrk3 - 133034897 133018921 79963 79963 95939 U 0 0
+chr1 135582677 135582828 NM_001159649_Lax1 - 135586665 135575626 0 3837 7051 . 1 0
+chr1 135582677 135582828 NM_144530_Zc3h11a - 135557956 135516445 24721 24721 66232 U 0 0
+chr1 135582677 135582828 NM_213616_Atp2b4 - 135697538 135602265 19437 114710 19437 D 0 0
+chr1 135582677 135582828 --- --- --- --- --- --- --- --- --- ---
+chr1 135851853 135852218 NM_054077_Prelp - 135865173 135806855 0 12955 44998 . 1 0
+chr1 135851853 135852218 NM_054076_Optc - 135805299 135787973 46554 46554 63880 U 0 0
+chr1 135851853 135852218 --- --- --- --- --- --- --- --- --- ---
+chr1 135851853 135852218 --- --- --- --- --- --- --- --- --- ---
+chr1 136956468 136956598 NM_007955_Ptprv - 137029151 137004306 47708 72553 47708 D 0 0
+chr1 136956468 136956598 NM_026823_Arl8a + 137043216 137053347 86618 86618 96749 U 0 0
+chr1 136956468 136956598 NM_026024_Ube2t + 136857731 136870739 85729 98737 85729 D 0 0
+chr1 136956468 136956598 NM_134438_Gpr37l1 - 137069087 137054243 97645 112489 97645 D 0 0
+chr1 13829227 13829564 --- --- --- --- --- --- --- --- --- ---
+chr1 13829227 13829564 --- --- --- --- --- --- --- --- --- ---
+chr1 13829227 13829564 --- --- --- --- --- --- --- --- --- ---
+chr1 13829227 13829564 --- --- --- --- --- --- --- --- --- ---
+chr1 138437726 138437860 NM_177643_Zfp281 + 138487073 138526617 49213 49213 88757 U 0 0
+chr1 138437726 138437860 --- --- --- --- --- --- --- --- --- ---
+chr1 138437726 138437860 --- --- --- --- --- --- --- --- --- ---
+chr1 138437726 138437860 --- --- --- --- --- --- --- --- --- ---
+chr1 140381656 140381785 --- --- --- --- --- --- --- --- --- ---
+chr1 140381656 140381785 --- --- --- --- --- --- --- --- --- ---
+chr1 140381656 140381785 --- --- --- --- --- --- --- --- --- ---
+chr1 140381656 140381785 --- --- --- --- --- --- --- --- --- ---
+chr1 145591041 145591176 NM_001038592_Glrx2 + 145585774 145608282 0 5267 17106 . 1 0
+chr1 145591041 145591176 NM_019562_Uchl5 + 145623774 145654586 32598 32598 63410 U 0 0
+chr1 145591041 145591176 NM_013835_Trove2 - 145624178 145597816 6640 33002 6640 D 0 0
+chr1 145591041 145591176 NM_145991_Cdc73 - 145549936 145274292 41105 41105 316749 U 0 0
+chr1 154971572 154971673 NM_008485_Lamc2 - 155033557 154969890 0 61884 1682 . 1 0
+chr1 154971572 154971673 --- --- --- --- --- --- --- --- --- ---
+chr1 154971572 154971673 --- --- --- --- --- --- --- --- --- ---
+chr1 154971572 154971673 --- --- --- --- --- --- --- --- --- ---
+chr1 155123313 155123435 NM_010683_Lamc1 - 155179906 155065803 0 56471 57510 . 1 0
+chr1 155123313 155123435 NM_008485_Lamc2 - 155033557 154969890 89756 89756 153423 U 0 0
+chr1 155123313 155123435 --- --- --- --- --- --- --- --- --- ---
+chr1 155123313 155123435 --- --- --- --- --- --- --- --- --- ---
+chr1 158510523 158510813 NM_009230_Soat1 - 158417632 158354679 92891 92891 155844 U 0 0
+chr1 158510523 158510813 NM_023141_Tor3a - 158604477 158583760 72947 93664 72947 D 0 0
+chr1 158510523 158510813 --- --- --- --- --- --- --- --- --- ---
+chr1 158510523 158510813 --- --- --- --- --- --- --- --- --- ---
+chr1 158537267 158537411 NM_023141_Tor3a - 158604477 158583760 46349 67066 46349 D 0 0
+chr1 158537267 158537411 NM_145413_Fam20b - 158649180 158608676 71265 111769 71265 D 0 0
+chr1 158537267 158537411 NM_009230_Soat1 - 158417632 158354679 119635 119635 182588 U 0 0
+chr1 158537267 158537411 --- --- --- --- --- --- --- --- --- ---
+chr1 158580638 158580759 NM_023141_Tor3a - 158604477 158583760 3001 23718 3001 D 0 0
+chr1 158580638 158580759 NM_145413_Fam20b - 158649180 158608676 27917 68421 27917 D 0 0
+chr1 158580638 158580759 --- --- --- --- --- --- --- --- --- ---
+chr1 158580638 158580759 --- --- --- --- --- --- --- --- --- ---
+chr1 158835251 158835391 NM_028333_Angptl1 + 158769061 158791209 44042 66190 44042 D 0 0
+chr1 158835251 158835391 --- --- --- --- --- --- --- --- --- ---
+chr1 158835251 158835391 --- --- --- --- --- --- --- --- --- ---
+chr1 158835251 158835391 --- --- --- --- --- --- --- --- --- ---
+chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 U 0 0
+chr1 159240736 159240866 --- --- --- --- --- --- --- --- --- ---
+chr1 159240736 159240866 --- --- --- --- --- --- --- --- --- ---
+chr1 159240736 159240866 --- --- --- --- --- --- --- --- --- ---
+chr1 163827897 163828062 NM_026078_Pigc + 163860747 163957217 32685 32685 129155 U 0 0
+chr1 163827897 163828062 NM_010177_Fasl - 163718844 163710820 109053 109053 117077 U 0 0
+chr1 163827897 163828062 --- --- --- --- --- --- --- --- --- ---
+chr1 163827897 163828062 --- --- --- --- --- --- --- --- --- ---
+chr1 164215623 164215935 NR_002870_Dnm3os + 164119785 164155671 59952 95838 59952 D 0 0
+chr1 164215623 164215935 --- --- --- --- --- --- --- --- --- ---
+chr1 164215623 164215935 --- --- --- --- --- --- --- --- --- ---
+chr1 164215623 164215935 --- --- --- --- --- --- --- --- --- ---
+chr1 167222964 167223261 NM_145513_Tiprl - 167183116 167133855 39848 39848 89109 U 0 0
+chr1 167222964 167223261 NM_145512_Sft2d2 - 167124549 167104119 98415 98415 118845 U 0 0
+chr1 167222964 167223261 --- --- --- --- --- --- --- --- --- ---
+chr1 167222964 167223261 --- --- --- --- --- --- --- --- --- ---
+chr1 167906284 167906554 NM_198934_Pou2f1 - 167932753 167804181 0 26199 102103 . 1 0
+chr1 167906284 167906554 --- --- --- --- --- --- --- --- --- ---
+chr1 167906284 167906554 --- --- --- --- --- --- --- --- --- ---
+chr1 167906284 167906554 --- --- --- --- --- --- --- --- --- ---
+chr1 170255081 170255260 --- --- --- --- --- --- --- --- --- ---
+chr1 170255081 170255260 --- --- --- --- --- --- --- --- --- ---
+chr1 170255081 170255260 --- --- --- --- --- --- --- --- --- ---
+chr1 170255081 170255260 --- --- --- --- --- --- --- --- --- ---
+chr1 17030405 17030545 NM_020604_Jph1 - 17087942 16837549 0 57397 192856 . 1 0
+chr1 17030405 17030545 NM_010267_Gdap1 + 17135463 17385513 104918 104918 354968 U 0 0
+chr1 17030405 17030545 --- --- --- --- --- --- --- --- --- ---
+chr1 17030405 17030545 --- --- --- --- --- --- --- --- --- ---
+chr1 172620779 172620912 NM_177068_Olfml2b + 172569075 172612915 7864 51704 7864 D 0 0
+chr1 172620779 172620912 --- --- --- --- --- --- --- --- --- ---
+chr1 172620779 172620912 --- --- --- --- --- --- --- --- --- ---
+chr1 172620779 172620912 --- --- --- --- --- --- --- --- --- ---
+chr1 172620917 172621080 NM_177068_Olfml2b + 172569075 172612915 8002 51842 8002 D 0 0
+chr1 172620917 172621080 --- --- --- --- --- --- --- --- --- ---
+chr1 172620917 172621080 --- --- --- --- --- --- --- --- --- ---
+chr1 172620917 172621080 --- --- --- --- --- --- --- --- --- ---
+chr1 174376470 174376659 NM_029612_Slamf9 + 174392516 174408706 15857 15857 32047 U 0 0
+chr1 174376470 174376659 NM_033608_Igsf9 + 174411686 174429005 35027 35027 52346 U 0 0
+chr1 174376470 174376659 NM_178598_Tagln2 + 174430123 174475991 53464 53464 99332 U 0 0
+chr1 174376470 174376659 NM_026234_Pigm + 174306609 174314210 62260 69861 62260 D 0 0
+chr1 181061299 181061446 --- --- --- --- --- --- --- --- --- ---
+chr1 181061299 181061446 --- --- --- --- --- --- --- --- --- ---
+chr1 181061299 181061446 --- --- --- --- --- --- --- --- --- ---
+chr1 181061299 181061446 --- --- --- --- --- --- --- --- --- ---
+chr1 182479646 182479905 NM_007415_Parp1 + 182499033 182531385 19128 19128 51480 U 0 0
+chr1 182479646 182479905 NM_001103182_Lin9 + 182572002 182620816 92097 92097 140911 U 0 0
+chr1 182479646 182479905 --- --- --- --- --- --- --- --- --- ---
+chr1 182479646 182479905 --- --- --- --- --- --- --- --- --- ---
+chr1 185854947 185855105 NM_022019_Dusp10 + 185755009 185899515 0 99938 44410 . 1 0
+chr1 185854947 185855105 --- --- --- --- --- --- --- --- --- ---
+chr1 185854947 185855105 --- --- --- --- --- --- --- --- --- ---
+chr1 185854947 185855105 --- --- --- --- --- --- --- --- --- ---
+chr1 194258648 194259032 --- --- --- --- --- --- --- --- --- ---
+chr1 194258648 194259032 --- --- --- --- --- --- --- --- --- ---
+chr1 194258648 194259032 --- --- --- --- --- --- --- --- --- ---
+chr1 194258648 194259032 --- --- --- --- --- --- --- --- --- ---
+chr1 194645118 194645475 NM_144881_Hhat - 194649833 194320603 0 4358 324515 . 1 0
+chr1 194645118 194645475 ENSMUST00000057543_A730013G03Rik - 194661397 194659323 13848 15922 13848 D 0 0
+chr1 194645118 194645475 NM_198247_Sertad4 - 194693726 194670313 24838 48251 24838 D 0 0
+chr1 194645118 194645475 --- --- --- --- --- --- --- --- --- ---
+chr1 194957396 194957723 NM_145415_AA408296 - 194956446 194918802 950 950 38594 U 0 1
+chr1 194957396 194957723 NM_016851_Irf6 + 194979326 194998230 21603 21603 40507 U 0 0
+chr1 194957396 194957723 BC055955_A130010J15Rik + 194999663 195004015 41940 41940 46292 U 0 0
+chr1 194957396 194957723 NM_153137_Traf3ip3 - 195027877 195001656 43933 70154 43933 D 0 0
+chr1 195324443 195324741 NM_144817_Camk1g - 195216632 195172540 107811 107811 151903 U 0 0
+chr1 195324443 195324741 --- --- --- --- --- --- --- --- --- ---
+chr1 195324443 195324741 --- --- --- --- --- --- --- --- --- ---
+chr1 195324443 195324741 --- --- --- --- --- --- --- --- --- ---
+chr1 195330701 195330930 NM_144817_Camk1g - 195216632 195172540 114069 114069 158161 U 0 0
+chr1 195330701 195330930 --- --- --- --- --- --- --- --- --- ---
+chr1 195330701 195330930 --- --- --- --- --- --- --- --- --- ---
+chr1 195330701 195330930 --- --- --- --- --- --- --- --- --- ---
+chr1 195338316 195338616 NM_144817_Camk1g - 195216632 195172540 121684 121684 165776 U 0 0
+chr1 195338316 195338616 --- --- --- --- --- --- --- --- --- ---
+chr1 195338316 195338616 --- --- --- --- --- --- --- --- --- ---
+chr1 195338316 195338616 --- --- --- --- --- --- --- --- --- ---
+chr1 195342728 195342985 NM_144817_Camk1g - 195216632 195172540 126096 126096 170188 U 0 0
+chr1 195342728 195342985 --- --- --- --- --- --- --- --- --- ---
+chr1 195342728 195342985 --- --- --- --- --- --- --- --- --- ---
+chr1 195342728 195342985 --- --- --- --- --- --- --- --- --- ---
+chr1 195384767 195385195 --- --- --- --- --- --- --- --- --- ---
+chr1 195384767 195385195 --- --- --- --- --- --- --- --- --- ---
+chr1 195384767 195385195 --- --- --- --- --- --- --- --- --- ---
+chr1 195384767 195385195 --- --- --- --- --- --- --- --- --- ---
+chr1 197057796 197057843 NM_007758_Cr2 - 197003002 196963005 54794 54794 94791 U 0 0
+chr1 197057796 197057843 NM_013499_Cr1l - 196957754 196924298 100042 100042 133498 U 0 0
+chr1 197057796 197057843 --- --- --- --- --- --- --- --- --- ---
+chr1 197057796 197057843 --- --- --- --- --- --- --- --- --- ---
+chr1 24609562 24609623 NM_007733_Col19a1 - 24602262 24258667 7300 7300 350895 U 0 0
+chr1 24609562 24609623 NM_026719_Lmbrd1 + 24593456 24847969 0 16106 238346 . 1 0
+chr1 24609562 24609623 --- --- --- --- --- --- --- --- --- ---
+chr1 24609562 24609623 --- --- --- --- --- --- --- --- --- ---
+chr1 24609923 24609992 NM_007733_Col19a1 - 24602262 24258667 7661 7661 351256 U 0 0
+chr1 24609923 24609992 NM_026719_Lmbrd1 + 24593456 24847969 0 16467 237977 . 1 0
+chr1 24609923 24609992 --- --- --- --- --- --- --- --- --- ---
+chr1 24609923 24609992 --- --- --- --- --- --- --- --- --- ---
+chr1 24730996 24731077 NM_026719_Lmbrd1 + 24820582 24823143 89505 89505 92066 U 0 0
+chr1 24730996 24731077 NM_007733_Col19a1 - 24602262 24258667 128734 128734 472329 U 0 0
+chr1 24730996 24731077 --- --- --- --- --- --- --- --- --- ---
+chr1 24730996 24731077 --- --- --- --- --- --- --- --- --- ---
+chr1 26734195 26734485 --- --- --- --- --- --- --- --- --- ---
+chr1 26734195 26734485 --- --- --- --- --- --- --- --- --- ---
+chr1 26734195 26734485 --- --- --- --- --- --- --- --- --- ---
+chr1 26734195 26734485 --- --- --- --- --- --- --- --- --- ---
+chr1 34206924 34207100 --- --- --- --- --- --- --- --- --- ---
+chr1 34206924 34207100 --- --- --- --- --- --- --- --- --- ---
+chr1 34206924 34207100 --- --- --- --- --- --- --- --- --- ---
+chr1 34206924 34207100 --- --- --- --- --- --- --- --- --- ---
+chr1 36106813 36107058 NM_015818_Hs6st1 + 36125255 36163289 18197 18197 56231 U 0 0
+chr1 36106813 36107058 --- --- --- --- --- --- --- --- --- ---
+chr1 36106813 36107058 --- --- --- --- --- --- --- --- --- ---
+chr1 36106813 36107058 --- --- --- --- --- --- --- --- --- ---
+chr1 39492140 39492513 NM_018775_Tbc1d8 - 39544345 39428350 0 51832 63790 . 1 0
+chr1 39492140 39492513 NM_053257_Rpl31 + 39421000 39429094 63046 71140 63046 D 0 0
+chr1 39492140 39492513 BC049091_D1Bwg0212e + 39592545 39603734 100032 100032 111221 U 0 0
+chr1 39492140 39492513 --- --- --- --- --- --- --- --- --- ---
+chr1 40325917 40326123 NM_008362_Il1r1 + 40274145 40373439 0 51772 47316 . 1 0
+chr1 40325917 40326123 NM_133193_Il1rl2 + 40381454 40447345 55331 55331 121222 U 0 0
+chr1 40325917 40326123 --- --- --- --- --- --- --- --- --- ---
+chr1 40325917 40326123 --- --- --- --- --- --- --- --- --- ---
+chr1 44195449 44195639 NM_011729_Ercc5 + 44204270 44256568 8631 8631 60929 U 0 0
+chr1 44195449 44195639 NM_023645_Kdelc1 - 44177102 44143458 18347 18347 51991 U 0 0
+chr1 44195449 44195639 NM_144558_Bivm + 44175822 44201615 0 19627 5976 . 1 0
+chr1 44195449 44195639 --- --- --- --- --- --- --- --- --- ---
+chr1 52625416 52625560 NM_008667_Nab1 - 52611216 52487127 14200 14200 138289 U 0 0
+chr1 52625416 52625560 NM_001142647_Tmem194b + 52687569 52708760 62009 62009 83200 U 0 0
+chr1 52625416 52625560 --- --- --- --- --- --- --- --- --- ---
+chr1 52625416 52625560 --- --- --- --- --- --- --- --- --- ---
+chr1 54631692 54631815 ENSMUST00000094950_Pgap1 - 54614539 54529849 17153 17153 101843 U 0 0
+chr1 54631692 54631815 --- --- --- --- --- --- --- --- --- ---
+chr1 54631692 54631815 --- --- --- --- --- --- --- --- --- ---
+chr1 54631692 54631815 --- --- --- --- --- --- --- --- --- ---
+chr1 55283572 55283675 NM_028713_Rftn2 - 55283748 55227030 0 73 56542 . 1 1
+chr1 55283572 55283675 NM_175439_Mars2 + 55294084 55297625 10409 10409 13950 U 0 0
+chr1 55283572 55283675 NM_025283_Mobkl3 + 55187734 55211736 71836 95838 71836 D 0 0
+chr1 55283572 55283675 --- --- --- --- --- --- --- --- --- ---
+chr1 63664888 63665018 NM_011780_Adam23 + 63640970 63642850 22038 23918 22038 D 0 0
+chr1 63664888 63665018 NM_029696_Mdh1b - 63776894 63745401 80383 111876 80383 D 0 0
+chr1 63664888 63665018 NM_172422_Fastkd2 + 63777134 63803028 112116 112116 138010 U 0 0
+chr1 63664888 63665018 --- --- --- --- --- --- --- --- --- ---
+chr1 72769824 72770056 NM_176980_Ankar - 72747143 72689581 22681 22681 80243 U 0 0
+chr1 72769824 72770056 NM_008342_Igfbp2 + 72840313 72899038 70257 70257 128982 U 0 0
+chr1 72769824 72770056 --- --- --- --- --- --- --- --- --- ---
+chr1 72769824 72770056 --- --- --- --- --- --- --- --- --- ---
+chr1 72770058 72770226 NM_176980_Ankar - 72747143 72689581 22915 22915 80477 U 0 0
+chr1 72770058 72770226 NM_008342_Igfbp2 + 72840313 72899038 70087 70087 128812 U 0 0
+chr1 72770058 72770226 --- --- --- --- --- --- --- --- --- ---
+chr1 72770058 72770226 --- --- --- --- --- --- --- --- --- ---
+chr1 72815517 72815742 NM_008342_Igfbp2 + 72840313 72899038 24571 24571 83296 U 0 0
+chr1 72815517 72815742 NM_176980_Ankar - 72747143 72689581 68374 68374 125936 U 0 0
+chr1 72815517 72815742 NM_010518_Igfbp5 - 72921468 72904507 88765 105726 88765 D 0 0
+chr1 72815517 72815742 --- --- --- --- --- --- --- --- --- ---
+chr1 75481920 75482054 NM_001001565_Chpf - 75476437 75470923 5483 5483 10997 U 0 0
+chr1 75481920 75482054 NM_178884_Obsl1 - 75503218 75482401 347 21164 347 D 0 0
+chr1 75481920 75482054 NM_010564_Inha + 75503647 75506924 21593 21593 24870 U 0 0
+chr1 75481920 75482054 NM_183022_Accn4 + 75447063 75470207 11713 34857 11713 D 0 0
+chr1 77457642 77457791 NM_007936_Epha4 - 77511653 77280640 0 53862 177002 . 1 0
+chr1 77457642 77457791 --- --- --- --- --- --- --- --- --- ---
+chr1 77457642 77457791 --- --- --- --- --- --- --- --- --- ---
+chr1 77457642 77457791 --- --- --- --- --- --- --- --- --- ---
+chr1 78630893 78631160 NM_028817_Acsl3 + 78654388 78743434 23228 23228 112274 U 0 0
+chr1 78630893 78631160 NM_011811_Farsb - 78506689 78414533 124204 124204 216360 U 0 0
+chr1 78630893 78631160 --- --- --- --- --- --- --- --- --- ---
+chr1 78630893 78631160 --- --- --- --- --- --- --- --- --- ---
+chr1 88408969 88409267 NM_172974_Cops7b + 88478926 88503950 69659 69659 94683 U 0 0
+chr1 88408969 88409267 NM_008801_Pde6d - 88479102 88427331 18064 69835 18064 D 0 0
+chr1 88408969 88409267 NM_010341_Nmur1 - 88297441 88282479 111528 111528 126490 U 0 0
+chr1 88408969 88409267 --- --- --- --- --- --- --- --- --- ---
+chr1 89989553 89989714 NM_201641_Ugt1a10 + 89922380 90115570 0 67173 125856 . 1 0
+chr1 89989553 89989714 NM_008299_Dnajb3 - 90102337 90101307 111593 112623 111593 D 0 0
+chr1 89989553 89989714 --- --- --- --- --- --- --- --- --- ---
+chr1 89989553 89989714 --- --- --- --- --- --- --- --- --- ---
+chr1 90412932 90413132 NM_008132_Glrp1 - 90406631 90396446 6301 6301 16486 U 0 0
+chr1 90412932 90413132 NM_029269_Spp2 + 90303568 90373213 39719 109364 39719 D 0 0
+chr1 90412932 90413132 --- --- --- --- --- --- --- --- --- ---
+chr1 90412932 90413132 --- --- --- --- --- --- --- --- --- ---
+chr1 90592499 90592629 NM_177305_Arl4c - 90617572 90569702 0 24943 22797 . 1 0
+chr1 90592499 90592629 --- --- --- --- --- --- --- --- --- ---
+chr1 90592499 90592629 --- --- --- --- --- --- --- --- --- ---
+chr1 90592499 90592629 --- --- --- --- --- --- --- --- --- ---
+chr1 91496003 91496145 --- --- --- --- --- --- --- --- --- ---
+chr1 91496003 91496145 --- --- --- --- --- --- --- --- --- ---
+chr1 91496003 91496145 --- --- --- --- --- --- --- --- --- ---
+chr1 91496003 91496145 --- --- --- --- --- --- --- --- --- ---
+chr1 91496155 91496319 --- --- --- --- --- --- --- --- --- ---
+chr1 91496155 91496319 --- --- --- --- --- --- --- --- --- ---
+chr1 91496155 91496319 --- --- --- --- --- --- --- --- --- ---
+chr1 91496155 91496319 --- --- --- --- --- --- --- --- --- ---
+chr1 92070253 92070431 NM_007722_Cxcr7 + 92100063 92112863 29632 29632 42432 U 0 0
+chr1 92070253 92070431 --- --- --- --- --- --- --- --- --- ---
+chr1 92070253 92070431 --- --- --- --- --- --- --- --- --- ---
+chr1 92070253 92070431 --- --- --- --- --- --- --- --- --- ---
+chr1 95186508 95186637 NM_178051_Mterfd2 - 95202630 95195779 9142 15993 9142 D 0 0
+chr1 95186508 95186637 NM_023200_Ppp1r7 + 95239431 95266345 52794 52794 79708 U 0 0
+chr1 95186508 95186637 NM_080850_Pask - 95240039 95205357 18720 53402 18720 D 0 0
+chr1 95186508 95186637 NM_172463_Sned1 + 95132418 95197642 0 54090 11005 . 1 0
+chr1 9619046 9619167 NM_178399_3110035E14Rik + 9591248 9617222 1824 27798 1824 D 0 0
+chr1 9619046 9619167 NM_008651_Mybl1 - 9690280 9635825 16658 71113 16658 D 0 0
+chr1 9619046 9619167 NM_175236_Adhfe1 + 9538049 9570746 48300 80997 48300 D 0 0
+chr1 9619046 9619167 NM_021511_Rrs1 + 9535513 9537532 81514 83533 81514 D 0 0
+chr1 9619175 9619382 NM_178399_3110035E14Rik + 9591248 9617222 1953 27927 1953 D 0 0
+chr1 9619175 9619382 NM_008651_Mybl1 - 9690280 9635825 16443 70898 16443 D 0 0
+chr1 9619175 9619382 NM_175236_Adhfe1 + 9538049 9570746 48429 81126 48429 D 0 0
+chr1 9619175 9619382 NM_021511_Rrs1 + 9535513 9537532 81643 83662 81643 D 0 0
diff -r 000000000000 -r 0abe6bac47a6 test-data/features_per_peak4.summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_per_peak4.summary Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,70 @@
+#peak.chr peak.start peak.end gene.id strand TSS TES dist_closest dist_TSS dist_TES direction overlap_gene overlap_promoter
+chr1 10617233 10617437 NM_177834_Cpa6 - 10710026 10314801 0 92589 302432 . 1 0
+chr1 108747519 108747791 NM_009190_Vps4b - 108739123 108665873 8396 8396 81646 U 0 0
+chr1 120760212 120760461 --- --- --- --- --- --- --- --- --- ---
+chr1 132950929 132951247 NM_010548_Il10 + 132916424 132921547 29382 34505 29382 D 0 0
+chr1 133114860 133115015 NM_018750_Rassf5 - 133144761 133072991 0 29746 41869 . 1 0
+chr1 135582677 135582828 NM_001159649_Lax1 - 135586665 135575626 0 3837 7051 . 1 0
+chr1 135851853 135852218 NM_054077_Prelp - 135865173 135806855 0 12955 44998 . 1 0
+chr1 136956468 136956598 NM_007955_Ptprv - 137029151 137004306 47708 72553 47708 D 0 0
+chr1 13829227 13829564 --- --- --- --- --- --- --- --- --- ---
+chr1 138437726 138437860 NM_177643_Zfp281 + 138487073 138526617 49213 49213 88757 U 0 0
+chr1 140381656 140381785 --- --- --- --- --- --- --- --- --- ---
+chr1 145591041 145591176 NM_001038592_Glrx2 + 145585774 145608282 0 5267 17106 . 1 0
+chr1 154971572 154971673 NM_008485_Lamc2 - 155033557 154969890 0 61884 1682 . 1 0
+chr1 155123313 155123435 NM_010683_Lamc1 - 155179906 155065803 0 56471 57510 . 1 0
+chr1 158510523 158510813 NM_009230_Soat1 - 158417632 158354679 92891 92891 155844 U 0 0
+chr1 158537267 158537411 NM_023141_Tor3a - 158604477 158583760 46349 67066 46349 D 0 0
+chr1 158580638 158580759 NM_023141_Tor3a - 158604477 158583760 3001 23718 3001 D 0 0
+chr1 158835251 158835391 NM_028333_Angptl1 + 158769061 158791209 44042 66190 44042 D 0 0
+chr1 159240736 159240866 BC055845_2810025M15Rik + 159342483 159350353 101617 101617 109487 U 0 0
+chr1 163827897 163828062 NM_026078_Pigc + 163860747 163957217 32685 32685 129155 U 0 0
+chr1 164215623 164215935 NR_002870_Dnm3os + 164119785 164155671 59952 95838 59952 D 0 0
+chr1 167222964 167223261 NM_145513_Tiprl - 167183116 167133855 39848 39848 89109 U 0 0
+chr1 167906284 167906554 NM_198934_Pou2f1 - 167932753 167804181 0 26199 102103 . 1 0
+chr1 170255081 170255260 --- --- --- --- --- --- --- --- --- ---
+chr1 17030405 17030545 NM_020604_Jph1 - 17087942 16837549 0 57397 192856 . 1 0
+chr1 172620779 172620912 NM_177068_Olfml2b + 172569075 172612915 7864 51704 7864 D 0 0
+chr1 172620917 172621080 NM_177068_Olfml2b + 172569075 172612915 8002 51842 8002 D 0 0
+chr1 174376470 174376659 NM_029612_Slamf9 + 174392516 174408706 15857 15857 32047 U 0 0
+chr1 181061299 181061446 --- --- --- --- --- --- --- --- --- ---
+chr1 182479646 182479905 NM_007415_Parp1 + 182499033 182531385 19128 19128 51480 U 0 0
+chr1 185854947 185855105 NM_022019_Dusp10 + 185755009 185899515 0 99938 44410 . 1 0
+chr1 194258648 194259032 --- --- --- --- --- --- --- --- --- ---
+chr1 194645118 194645475 NM_144881_Hhat - 194649833 194320603 0 4358 324515 . 1 0
+chr1 194957396 194957723 NM_145415_AA408296 - 194956446 194918802 950 950 38594 U 0 1
+chr1 195324443 195324741 NM_144817_Camk1g - 195216632 195172540 107811 107811 151903 U 0 0
+chr1 195330701 195330930 NM_144817_Camk1g - 195216632 195172540 114069 114069 158161 U 0 0
+chr1 195338316 195338616 NM_144817_Camk1g - 195216632 195172540 121684 121684 165776 U 0 0
+chr1 195342728 195342985 NM_144817_Camk1g - 195216632 195172540 126096 126096 170188 U 0 0
+chr1 195384767 195385195 --- --- --- --- --- --- --- --- --- ---
+chr1 197057796 197057843 NM_007758_Cr2 - 197003002 196963005 54794 54794 94791 U 0 0
+chr1 24609562 24609623 NM_007733_Col19a1 - 24602262 24258667 7300 7300 350895 U 0 0
+chr1 24609923 24609992 NM_007733_Col19a1 - 24602262 24258667 7661 7661 351256 U 0 0
+chr1 24730996 24731077 NM_026719_Lmbrd1 + 24820582 24823143 89505 89505 92066 U 0 0
+chr1 26734195 26734485 --- --- --- --- --- --- --- --- --- ---
+chr1 34206924 34207100 --- --- --- --- --- --- --- --- --- ---
+chr1 36106813 36107058 NM_015818_Hs6st1 + 36125255 36163289 18197 18197 56231 U 0 0
+chr1 39492140 39492513 NM_018775_Tbc1d8 - 39544345 39428350 0 51832 63790 . 1 0
+chr1 40325917 40326123 NM_008362_Il1r1 + 40274145 40373439 0 51772 47316 . 1 0
+chr1 44195449 44195639 NM_011729_Ercc5 + 44204270 44256568 8631 8631 60929 U 0 0
+chr1 52625416 52625560 NM_008667_Nab1 - 52611216 52487127 14200 14200 138289 U 0 0
+chr1 54631692 54631815 ENSMUST00000094950_Pgap1 - 54614539 54529849 17153 17153 101843 U 0 0
+chr1 55283572 55283675 NM_028713_Rftn2 - 55283748 55227030 0 73 56542 . 1 1
+chr1 63664888 63665018 NM_011780_Adam23 + 63640970 63642850 22038 23918 22038 D 0 0
+chr1 72769824 72770056 NM_176980_Ankar - 72747143 72689581 22681 22681 80243 U 0 0
+chr1 72770058 72770226 NM_176980_Ankar - 72747143 72689581 22915 22915 80477 U 0 0
+chr1 72815517 72815742 NM_008342_Igfbp2 + 72840313 72899038 24571 24571 83296 U 0 0
+chr1 75481920 75482054 NM_001001565_Chpf - 75476437 75470923 5483 5483 10997 U 0 0
+chr1 77457642 77457791 NM_007936_Epha4 - 77511653 77280640 0 53862 177002 . 1 0
+chr1 78630893 78631160 NM_028817_Acsl3 + 78654388 78743434 23228 23228 112274 U 0 0
+chr1 88408969 88409267 NM_172974_Cops7b + 88478926 88503950 69659 69659 94683 U 0 0
+chr1 89989553 89989714 NM_201641_Ugt1a10 + 89922380 90115570 0 67173 125856 . 1 0
+chr1 90412932 90413132 NM_008132_Glrp1 - 90406631 90396446 6301 6301 16486 U 0 0
+chr1 90592499 90592629 NM_177305_Arl4c - 90617572 90569702 0 24943 22797 . 1 0
+chr1 91496003 91496145 --- --- --- --- --- --- --- --- --- ---
+chr1 91496155 91496319 --- --- --- --- --- --- --- --- --- ---
+chr1 92070253 92070431 NM_007722_Cxcr7 + 92100063 92112863 29632 29632 42432 U 0 0
+chr1 95186508 95186637 NM_178051_Mterfd2 - 95202630 95195779 9142 15993 9142 D 0 0
+chr1 9619046 9619167 NM_178399_3110035E14Rik + 9591248 9617222 1824 27798 1824 D 0 0
+chr1 9619175 9619382 NM_178399_3110035E14Rik + 9591248 9617222 1953 27927 1953 D 0 0
diff -r 000000000000 -r 0abe6bac47a6 test-data/features_per_summit.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_per_summit.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,654 @@
+#peak.chr peak.start peak.end gene.id_1 strand_1 TSS_1 TES_1 dist_closest_1 dist_TSS_1 dist_TES_1 direction_1 overlap_gene_1 overlap_promoter_1 gene.id_2 strand_2 TSS_2 TES_2 dist_closest_2 dist_TSS_2 dist_TES_2 direction_2 overlap_gene_2 overlap_promoter_2 gene.id_3 strand_3 TSS_3 TES_3 dist_closest_3 dist_TSS_3 dist_TES_3 direction_3 overlap_gene_3 overlap_promoter_3 gene.id_4 strand_4 TSS_4 TES_4 dist_closest_4 dist_TSS_4 dist_TES_4 direction_4 overlap_gene_4 overlap_promoter_4
+chr10 106033584 106033585 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 106033751 106033752 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 107429926 107429927 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 114752719 114752720 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 114994096 114994097 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 127058840 127058841 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 127184557 127184558 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 13089536 13089537 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 13408622 13408623 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 17725474 17725475 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 21862583 21862584 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 21862774 21862775 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 31587625 31587626 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 41613298 41613299 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 43640892 43640893 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 43740181 43740182 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 45093322 45093323 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 57702300 57702301 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 59362596 59362597 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 59693654 59693655 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 60613588 60613589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 60696228 60696229 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 67567003 67567004 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 76664902 76664903 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 7707698 7707699 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 79808095 79808096 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 80126390 80126391 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 81033719 81033720 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 82306942 82306943 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 82517145 82517146 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 84922053 84922054 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 88433836 88433837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 89195191 89195192 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 93642365 93642366 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 94183365 94183366 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr10 94306306 94306307 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 10627335 10627336 NM_177834_Cpa6 - 10710026 10314801 0 82690 312534 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 108757655 108757656 NM_009257_Serpinb5 + 108757652 108779925 0 3 22269 . 1 1 NM_009190_Vps4b - 108739123 108665873 18532 18532 91782 U 0 0 NM_027971_Serpinb12 + 108831026 108853655 73370 73370 95999 U 0 0 NM_027534_Kdsr - 108656357 108617007 101298 101298 140648 U 0 0
+chr11 100148455 100148456 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 100964551 100964552 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 102973374 102973375 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 103196320 103196321 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 107278688 107278689 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 110241161 110241162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 114563829 114563830 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 115639021 115639022 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 115836265 115836266 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 119827740 119827741 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 120952392 120952393 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 121341339 121341340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 16560450 16560451 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 18798190 18798191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 19003164 19003165 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 20247624 20247625 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 120770337 120770338 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 21483462 21483463 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 29514477 29514478 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 3000481 3000482 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 3266659 3266660 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 132961088 132961089 NM_010548_Il10 + 132916424 132921547 39541 44664 39541 D 0 0 NM_001009940_Il19 - 132915234 132786042 45854 45854 175046 U 0 0 NM_008551_Mapkapk2 - 133013820 132950274 0 52731 10814 . 1 0 NM_145508_Dyrk3 - 133034897 133018921 57832 73808 57832 D 0 0
+chr1 133124938 133124939 NM_018750_Rassf5 - 133144761 133072991 0 19822 51947 . 1 0 NM_019777_Ikbke - 133176163 133151052 26113 51224 26113 D 0 0 NM_001136070_Lgtn + 133049773 133084235 40703 75165 40703 D 0 0 NM_145508_Dyrk3 - 133034897 133018921 90041 90041 106017 U 0 0
+chr11 34495361 34495362 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 135592753 135592754 NM_001159649_Lax1 - 135586665 135575626 6088 6088 17127 U 0 1 NM_144530_Zc3h11a - 135557956 135516445 34797 34797 76308 U 0 0 NM_213616_Atp2b4 - 135697538 135602265 9511 104784 9511 D 0 0 . . . . . . . . . .
+chr1 135862036 135862037 NM_054077_Prelp - 135865173 135806855 0 3136 55181 . 1 0 NM_054076_Optc - 135805299 135787973 56737 56737 74063 U 0 0 NM_007570_Btg2 - 135991759 135971251 109214 129722 109214 D 0 0 . . . . . . . . . .
+chr1 136966533 136966534 NM_007955_Ptprv - 137029151 137004306 37772 62617 37772 D 0 0 NM_026823_Arl8a + 137043216 137053347 76682 76682 86813 U 0 0 NM_134438_Gpr37l1 - 137069087 137054243 87709 102553 87709 D 0 0 NM_026024_Ube2t + 136857731 136870739 95794 108802 95794 D 0 0
+chr1 13839396 13839397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 138447793 138447794 NM_177643_Zfp281 + 138487073 138526617 39279 39279 78823 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 140391721 140391722 NM_021605_Nek7 - 140516775 140379472 0 125053 12249 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 4116866 4116867 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 145601109 145601110 NM_001038592_Glrx2 + 145585774 145608282 0 15335 7172 . 1 0 NM_019562_Uchl5 + 145623774 145654586 22664 22664 53476 U 0 0 NM_013835_Trove2 - 145624178 145597816 0 23068 3293 . 1 0 NM_145991_Cdc73 - 145549936 145274292 51173 51173 326817 U 0 0
+chr11 50300699 50300700 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 5481053 5481054 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 154981623 154981624 NM_008485_Lamc2 - 155033557 154969890 0 51933 11733 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 155133374 155133375 NM_010683_Lamc1 - 155179906 155065803 0 46531 67571 . 1 0 NM_008485_Lamc2 - 155033557 154969890 99817 99817 163484 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 158520668 158520669 NM_023141_Tor3a - 158604477 158583760 63091 83808 63091 D 0 0 NM_009230_Soat1 - 158417632 158354679 103036 103036 165989 U 0 0 NM_145413_Fam20b - 158649180 158608676 88007 128511 88007 D 0 0 . . . . . . . . . .
+chr1 158547339 158547340 NM_023141_Tor3a - 158604477 158583760 36420 57137 36420 D 0 0 NM_145413_Fam20b - 158649180 158608676 61336 101840 61336 D 0 0 NM_009230_Soat1 - 158417632 158354679 129707 129707 192660 U 0 0 . . . . . . . . . .
+chr1 158590699 158590700 NM_023141_Tor3a - 158604477 158583760 0 13777 6939 . 1 0 NM_145413_Fam20b - 158649180 158608676 17976 58480 17976 D 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 158845321 158845322 NM_028333_Angptl1 + 158769061 158791209 54112 76260 54112 D 0 0 NM_023884_Ralgps2 - 158969600 158734300 0 124278 111021 . 1 0 . . . . . . . . . . . . . . . . . . . .
+chr1 159250801 159250802 BC055845_2810025M15Rik + 159342483 159350353 91681 91681 99551 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 59272503 59272504 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 6069204 6069205 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 163837980 163837981 NM_026078_Pigc + 163860747 163957217 22766 22766 119236 U 0 0 NM_010177_Fasl - 163718844 163710820 119136 119136 127160 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 164225779 164225780 NR_002870_Dnm3os + 164119785 164155671 70108 105994 70108 D 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 167233113 167233114 NM_145513_Tiprl - 167183116 167133855 49997 49997 99258 U 0 0 NM_145512_Sft2d2 - 167124549 167104119 108564 108564 128994 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 167916419 167916420 NM_198934_Pou2f1 - 167932753 167804181 0 16333 112238 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 69572437 69572438 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 170265171 170265172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 70397406 70397407 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 17040475 17040476 NM_020604_Jph1 - 17087942 16837549 0 47466 202926 . 1 0 NM_010267_Gdap1 + 17135463 17385513 94987 94987 345037 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr1 172630846 172630847 NM_177068_Olfml2b + 172569075 172612915 17931 61771 17931 D 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 172630999 172631000 NM_177068_Olfml2b + 172569075 172612915 18084 61924 18084 D 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 174386565 174386566 NM_029612_Slamf9 + 174392516 174408706 5950 5950 22140 U 0 1 NM_033608_Igsf9 + 174411686 174429005 25120 25120 42439 U 0 0 NM_178598_Tagln2 + 174430123 174475991 43557 43557 89425 U 0 0 NM_026234_Pigm + 174306609 174314210 72355 79956 72355 D 0 0
+chr11 76126479 76126480 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 181071373 181071374 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 182489776 182489777 NM_007415_Parp1 + 182499033 182531385 9256 9256 41608 U 0 1 NM_001103182_Lin9 + 182572002 182620816 82225 82225 131039 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr11 83860977 83860978 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 84381942 84381943 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 8483612 8483613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 8541945 8541946 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 185865026 185865027 NM_022019_Dusp10 + 185755009 185899515 0 110017 34488 . 1 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 87257043 87257044 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 87967409 87967410 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 87967599 87967600 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 93986729 93986730 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 194268840 194268841 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 194655297 194655298 NM_144881_Hhat - 194649833 194320603 5464 5464 334694 U 0 1 ENSMUST00000057543_A730013G03Rik - 194661397 194659323 4025 6099 4025 D 0 0 NM_198247_Sertad4 - 194693726 194670313 15015 38428 15015 D 0 0 . . . . . . . . . .
+chr1 194967560 194967561 NM_145415_AA408296 - 194956446 194918802 11114 11114 48758 U 0 0 NM_016851_Irf6 + 194979326 194998230 11765 11765 30669 U 0 0 BC055955_A130010J15Rik + 194999663 195004015 32102 32102 36454 U 0 0 NM_153137_Traf3ip3 - 195027877 195001656 34095 60316 34095 D 0 0
+chr1 195334592 195334593 NM_144817_Camk1g - 195216632 195172540 117960 117960 162052 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195340816 195340817 NM_144817_Camk1g - 195216632 195172540 124184 124184 168276 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195348466 195348467 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195352857 195352858 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 195394981 195394982 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 197067820 197067821 NM_007758_Cr2 - 197003002 196963005 64818 64818 104815 U 0 0 NM_013499_Cr1l - 196957754 196924298 110066 110066 143522 U 0 0 . . . . . . . . . . . . . . . . . . . .
+chr11 97171690 97171691 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 97233548 97233549 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr11 97297212 97297213 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 104299157 104299158 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 106237696 106237697 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 106674392 106674393 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 112330425 112330426 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 112477144 112477145 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 112975712 112975713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 113981451 113981452 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 114119343 114119344 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 117853390 117853391 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 25562241 25562242 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 25648378 25648379 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 37211753 37211754 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 24619593 24619594 NM_007733_Col19a1 - 24602262 24258667 17331 17331 360926 U 0 0 NM_026719_Lmbrd1 + 24593456 24847969 0 26137 228375 . 1 0 . . . . . . . . . . . . . . . . . . . .
+chr1 24619958 24619959 NM_007733_Col19a1 - 24602262 24258667 17696 17696 361291 U 0 0 NM_026719_Lmbrd1 + 24593456 24847969 0 26502 228010 . 1 0 . . . . . . . . . . . . . . . . . . . .
+chr1 24741037 24741038 NM_026719_Lmbrd1 + 24820582 24823143 79544 79544 82105 U 0 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 57923295 57923296 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 58725309 58725310 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 26744340 26744341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 70755181 70755182 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 72971895 72971896 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr12 80608252 80608253 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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+chr8 129127362 129127363 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 129549456 129549457 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 13548998 13548999 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 13668465 13668466 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 14306960 14306961 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 17594804 17594805 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 19919526 19919527 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 19924810 19924811 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 22870138 22870139 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 23921280 23921281 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 24206095 24206096 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 34068894 34068895 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 37107644 37107645 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 4586605 4586606 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 70850825 70850826 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 71717281 71717282 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 73173598 73173599 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 73183558 73183559 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 73297497 73297498 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 81256455 81256456 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 86143616 86143617 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 87180694 87180695 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 88126748 88126749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 93828640 93828641 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr8 97699878 97699879 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 100543647 100543648 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 103988283 103988284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 106273656 106273657 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 107478162 107478163 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 108851463 108851464 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 110183808 110183809 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 111053664 111053665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 116828689 116828690 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 118884586 118884587 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 120883928 120883929 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 123371104 123371105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 13408238 13408239 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 14466849 14466850 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 14480293 14480294 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 24346538 24346539 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 3258857 3258858 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 42777363 42777364 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 43528251 43528252 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 43585984 43585985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 44215148 44215149 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 44307103 44307104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 54460731 54460732 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 66728918 66728919 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 66794084 66794085 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 67556540 67556541 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 70477636 70477637 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 72497695 72497696 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 72916030 72916031 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 74815214 74815215 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 75371664 75371665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 8033087 8033088 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 8055015 8055016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 83462792 83462793 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr9 86714892 86714893 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chrX 109484691 109484692 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chrX 137172820 137172821 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chrX 139917606 139917607 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chrX 140401017 140401018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chrX 163589625 163589626 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chrX 166360754 166360755 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chrX 166427362 166427363 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chrX 166432950 166432951 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chrX 84483714 84483715 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chrX 98516735 98516736 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_canonical_genes.data_manager_json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_canonical_genes.data_manager_json Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,1 @@
+{"data_tables": {"rnachipintegrator_canonical_genes": {"value": "dataset_62.dat", "name": "Mouse (mm9)", "dbkey": "mm9"}}}
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_canonical_genes.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_canonical_genes.tsv Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,10 @@
+mm9.kgXref.geneSymbol #mm9.knownCanonical.chrom mm9.knownCanonical.chromStart mm9.knownCanonical.chromEnd mm9.knownGene.strand mm9.knownCanonical.transcript mm9.kgXref.refseq
+Xkr4 chr1 3204562 3661579 - uc007aeu.1 NM_001011874
+AK149000 chr1 3638391 3648985 - uc007aev.1
+Rp1 chr1 4333587 4350395 - uc007aex.2 NM_011283
+Sox17 chr1 4481008 4486494 - uc007aez.1 NM_011441
+Mrpl15 chr1 4763278 4775807 - uc007aff.2 NM_001177658
+Lypla1 chr1 4797973 4836816 + uc007afh.1 NM_008866
+Tcea1 chr1 4847774 4887990 + uc007afi.2 NM_011541
+Rgs20 chr1 4899656 5060366 - uc007afl.2 NM_001177795
+Atp6v1h chr1 5073253 5152630 + uc007afn.1 NM_133826
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_features_per_peak.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_features_per_peak.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,502 @@
+#chr start end gene.id strand TSS TES dist_closest dist_TSS dist_TES direction overlap_gene.overlap_promoter
+chr1 3213477 3213513 --- --- --- --- --- --- --- --- --- ---
+chr1 3542857 3542893 --- --- --- --- --- --- --- --- --- ---
+chr1 3560979 3561015 --- --- --- --- --- --- --- --- --- ---
+chr1 3621547 3621583 AK149000 - 3648985 3638391 16808 27402 16808 D 0 0
+chr1 3621547 3621583 Xkr4 - 3661579 3204562 0 39996 416985 . 1 0
+chr1 4630453 4630489 --- --- --- --- --- --- --- --- --- ---
+chr1 5261737 5261773 --- --- --- --- --- --- --- --- --- ---
+chr1 5562257 5562293 --- --- --- --- --- --- --- --- --- ---
+chr1 6926999 6927035 --- --- --- --- --- --- --- --- --- ---
+chr1 7262846 7262882 --- --- --- --- --- --- --- --- --- ---
+chr1 7322487 7322523 --- --- --- --- --- --- --- --- --- ---
+chr1 7666187 7666223 --- --- --- --- --- --- --- --- --- ---
+chr1 7744070 7744106 --- --- --- --- --- --- --- --- --- ---
+chr1 7969291 7969327 --- --- --- --- --- --- --- --- --- ---
+chr1 8421057 8421093 --- --- --- --- --- --- --- --- --- ---
+chr1 8679021 8679057 --- --- --- --- --- --- --- --- --- ---
+chr1 9359611 9359647 --- --- --- --- --- --- --- --- --- ---
+chr1 9415439 9415475 --- --- --- --- --- --- --- --- --- ---
+chr1 9608130 9608166 --- --- --- --- --- --- --- --- --- ---
+chr1 9616803 9616839 --- --- --- --- --- --- --- --- --- ---
+chr1 9897397 9897433 --- --- --- --- --- --- --- --- --- ---
+chr1 10251725 10251761 --- --- --- --- --- --- --- --- --- ---
+chr1 10254195 10254231 --- --- --- --- --- --- --- --- --- ---
+chr1 10305254 10305290 --- --- --- --- --- --- --- --- --- ---
+chr1 10451286 10451322 --- --- --- --- --- --- --- --- --- ---
+chr1 11340573 11340609 --- --- --- --- --- --- --- --- --- ---
+chr1 11610483 11610519 --- --- --- --- --- --- --- --- --- ---
+chr1 11960381 11960417 --- --- --- --- --- --- --- --- --- ---
+chr1 11987310 11987346 --- --- --- --- --- --- --- --- --- ---
+chr1 12441678 12441714 --- --- --- --- --- --- --- --- --- ---
+chr1 12704380 12704416 --- --- --- --- --- --- --- --- --- ---
+chr1 12871650 12871686 --- --- --- --- --- --- --- --- --- ---
+chr1 13179280 13179316 --- --- --- --- --- --- --- --- --- ---
+chr1 13934524 13934560 --- --- --- --- --- --- --- --- --- ---
+chr1 14479277 14479313 --- --- --- --- --- --- --- --- --- ---
+chr1 14755996 14756032 --- --- --- --- --- --- --- --- --- ---
+chr1 14848637 14848673 --- --- --- --- --- --- --- --- --- ---
+chr1 14967919 14967955 --- --- --- --- --- --- --- --- --- ---
+chr1 15097029 15097065 --- --- --- --- --- --- --- --- --- ---
+chr1 17128114 17128150 --- --- --- --- --- --- --- --- --- ---
+chr1 17160496 17160532 --- --- --- --- --- --- --- --- --- ---
+chr1 17334281 17334317 --- --- --- --- --- --- --- --- --- ---
+chr1 17605285 17605321 --- --- --- --- --- --- --- --- --- ---
+chr1 17922903 17922939 --- --- --- --- --- --- --- --- --- ---
+chr1 18681561 18681597 --- --- --- --- --- --- --- --- --- ---
+chr1 19213304 19213340 --- --- --- --- --- --- --- --- --- ---
+chr1 20317581 20317617 --- --- --- --- --- --- --- --- --- ---
+chr1 21466434 21466470 --- --- --- --- --- --- --- --- --- ---
+chr1 22074908 22074944 --- --- --- --- --- --- --- --- --- ---
+chr1 22696516 22696552 --- --- --- --- --- --- --- --- --- ---
+chr1 23655828 23655864 --- --- --- --- --- --- --- --- --- ---
+chr1 24583893 24583929 --- --- --- --- --- --- --- --- --- ---
+chr1 24738828 24738864 --- --- --- --- --- --- --- --- --- ---
+chr1 24743796 24743832 --- --- --- --- --- --- --- --- --- ---
+chr1 25009857 25009893 --- --- --- --- --- --- --- --- --- ---
+chr1 25313509 25313545 --- --- --- --- --- --- --- --- --- ---
+chr1 26503310 26503346 --- --- --- --- --- --- --- --- --- ---
+chr1 27025916 27025952 --- --- --- --- --- --- --- --- --- ---
+chr1 27385857 27385893 --- --- --- --- --- --- --- --- --- ---
+chr1 27598627 27598663 --- --- --- --- --- --- --- --- --- ---
+chr1 27636264 27636300 --- --- --- --- --- --- --- --- --- ---
+chr1 27687524 27687560 --- --- --- --- --- --- --- --- --- ---
+chr1 28357424 28357460 --- --- --- --- --- --- --- --- --- ---
+chr1 29135026 29135062 --- --- --- --- --- --- --- --- --- ---
+chr1 29633575 29633611 --- --- --- --- --- --- --- --- --- ---
+chr1 29825940 29825976 --- --- --- --- --- --- --- --- --- ---
+chr1 30137793 30137829 --- --- --- --- --- --- --- --- --- ---
+chr1 30142141 30142177 --- --- --- --- --- --- --- --- --- ---
+chr1 30465754 30465790 --- --- --- --- --- --- --- --- --- ---
+chr1 30785908 30785944 --- --- --- --- --- --- --- --- --- ---
+chr1 31077695 31077731 --- --- --- --- --- --- --- --- --- ---
+chr1 31123645 31123681 --- --- --- --- --- --- --- --- --- ---
+chr1 31158742 31158778 --- --- --- --- --- --- --- --- --- ---
+chr1 31883682 31883718 --- --- --- --- --- --- --- --- --- ---
+chr1 31990075 31990111 --- --- --- --- --- --- --- --- --- ---
+chr1 33079863 33079899 --- --- --- --- --- --- --- --- --- ---
+chr1 33288587 33288623 --- --- --- --- --- --- --- --- --- ---
+chr1 33856089 33856125 --- --- --- --- --- --- --- --- --- ---
+chr1 34588477 34588513 --- --- --- --- --- --- --- --- --- ---
+chr1 34633149 34633185 --- --- --- --- --- --- --- --- --- ---
+chr1 34749000 34749036 --- --- --- --- --- --- --- --- --- ---
+chr1 34764419 34764455 --- --- --- --- --- --- --- --- --- ---
+chr1 35032286 35032322 --- --- --- --- --- --- --- --- --- ---
+chr1 35047073 35047109 --- --- --- --- --- --- --- --- --- ---
+chr1 35933401 35933437 --- --- --- --- --- --- --- --- --- ---
+chr1 36135485 36135521 --- --- --- --- --- --- --- --- --- ---
+chr1 36742521 36742557 --- --- --- --- --- --- --- --- --- ---
+chr1 36859752 36859788 --- --- --- --- --- --- --- --- --- ---
+chr1 37388614 37388650 --- --- --- --- --- --- --- --- --- ---
+chr1 37763263 37763299 --- --- --- --- --- --- --- --- --- ---
+chr1 37824535 37824571 --- --- --- --- --- --- --- --- --- ---
+chr1 37974386 37974422 --- --- --- --- --- --- --- --- --- ---
+chr1 37994576 37994612 --- --- --- --- --- --- --- --- --- ---
+chr1 38460553 38460589 --- --- --- --- --- --- --- --- --- ---
+chr1 38502464 38502500 --- --- --- --- --- --- --- --- --- ---
+chr1 38761349 38761385 --- --- --- --- --- --- --- --- --- ---
+chr1 38832604 38832640 --- --- --- --- --- --- --- --- --- ---
+chr1 39388554 39388590 --- --- --- --- --- --- --- --- --- ---
+chr1 39439044 39439080 --- --- --- --- --- --- --- --- --- ---
+chr1 39593773 39593809 --- --- --- --- --- --- --- --- --- ---
+chr1 39693273 39693309 --- --- --- --- --- --- --- --- --- ---
+chr1 39924300 39924336 --- --- --- --- --- --- --- --- --- ---
+chr1 40132160 40132196 --- --- --- --- --- --- --- --- --- ---
+chr1 40243823 40243859 --- --- --- --- --- --- --- --- --- ---
+chr1 40426457 40426493 --- --- --- --- --- --- --- --- --- ---
+chr1 40773529 40773565 --- --- --- --- --- --- --- --- --- ---
+chr1 40785687 40785723 --- --- --- --- --- --- --- --- --- ---
+chr1 40953366 40953402 --- --- --- --- --- --- --- --- --- ---
+chr1 41021129 41021165 --- --- --- --- --- --- --- --- --- ---
+chr1 41080072 41080108 --- --- --- --- --- --- --- --- --- ---
+chr1 41138125 41138161 --- --- --- --- --- --- --- --- --- ---
+chr1 41154639 41154675 --- --- --- --- --- --- --- --- --- ---
+chr1 42299563 42299599 --- --- --- --- --- --- --- --- --- ---
+chr1 42463569 42463605 --- --- --- --- --- --- --- --- --- ---
+chr1 42518766 42518802 --- --- --- --- --- --- --- --- --- ---
+chr1 43783219 43783255 --- --- --- --- --- --- --- --- --- ---
+chr1 44575305 44575341 --- --- --- --- --- --- --- --- --- ---
+chr1 44600563 44600599 --- --- --- --- --- --- --- --- --- ---
+chr1 44982842 44982878 --- --- --- --- --- --- --- --- --- ---
+chr1 45305515 45305551 --- --- --- --- --- --- --- --- --- ---
+chr1 45339758 45339794 --- --- --- --- --- --- --- --- --- ---
+chr1 45422086 45422122 --- --- --- --- --- --- --- --- --- ---
+chr1 45824016 45824052 --- --- --- --- --- --- --- --- --- ---
+chr1 46360753 46360789 --- --- --- --- --- --- --- --- --- ---
+chr1 46527798 46527834 --- --- --- --- --- --- --- --- --- ---
+chr1 47047692 47047728 --- --- --- --- --- --- --- --- --- ---
+chr1 48153542 48153578 --- --- --- --- --- --- --- --- --- ---
+chr1 48306038 48306074 --- --- --- --- --- --- --- --- --- ---
+chr1 48454759 48454795 --- --- --- --- --- --- --- --- --- ---
+chr1 49437523 49437559 --- --- --- --- --- --- --- --- --- ---
+chr1 49709489 49709525 --- --- --- --- --- --- --- --- --- ---
+chr1 50863175 50863211 --- --- --- --- --- --- --- --- --- ---
+chr1 50927909 50927945 --- --- --- --- --- --- --- --- --- ---
+chr1 51137708 51137744 --- --- --- --- --- --- --- --- --- ---
+chr1 51204752 51204788 --- --- --- --- --- --- --- --- --- ---
+chr1 51769267 51769303 --- --- --- --- --- --- --- --- --- ---
+chr1 52110888 52110924 --- --- --- --- --- --- --- --- --- ---
+chr1 52123042 52123078 --- --- --- --- --- --- --- --- --- ---
+chr1 52272863 52272899 --- --- --- --- --- --- --- --- --- ---
+chr1 52840700 52840736 --- --- --- --- --- --- --- --- --- ---
+chr1 52890780 52890816 --- --- --- --- --- --- --- --- --- ---
+chr1 53450997 53451033 --- --- --- --- --- --- --- --- --- ---
+chr1 53599262 53599298 --- --- --- --- --- --- --- --- --- ---
+chr1 53784753 53784789 --- --- --- --- --- --- --- --- --- ---
+chr1 53990993 53991029 --- --- --- --- --- --- --- --- --- ---
+chr1 54016877 54016913 --- --- --- --- --- --- --- --- --- ---
+chr1 54073194 54073230 --- --- --- --- --- --- --- --- --- ---
+chr1 54258499 54258535 --- --- --- --- --- --- --- --- --- ---
+chr1 54429617 54429653 --- --- --- --- --- --- --- --- --- ---
+chr1 54526981 54527017 --- --- --- --- --- --- --- --- --- ---
+chr1 54655149 54655185 --- --- --- --- --- --- --- --- --- ---
+chr1 55664918 55664954 --- --- --- --- --- --- --- --- --- ---
+chr1 55720320 55720356 --- --- --- --- --- --- --- --- --- ---
+chr1 55720320 55720356 --- --- --- --- --- --- --- --- --- ---
+chr1 56585857 56585893 --- --- --- --- --- --- --- --- --- ---
+chr1 56639054 56639090 --- --- --- --- --- --- --- --- --- ---
+chr1 56791957 56791993 --- --- --- --- --- --- --- --- --- ---
+chr1 57250654 57250690 --- --- --- --- --- --- --- --- --- ---
+chr1 57825391 57825427 --- --- --- --- --- --- --- --- --- ---
+chr1 58106272 58106308 --- --- --- --- --- --- --- --- --- ---
+chr1 58642339 58642375 --- --- --- --- --- --- --- --- --- ---
+chr1 58778630 58778666 --- --- --- --- --- --- --- --- --- ---
+chr1 59053239 59053275 --- --- --- --- --- --- --- --- --- ---
+chr1 59066499 59066535 --- --- --- --- --- --- --- --- --- ---
+chr1 59162431 59162467 --- --- --- --- --- --- --- --- --- ---
+chr1 59271155 59271191 --- --- --- --- --- --- --- --- --- ---
+chr1 59457887 59457923 --- --- --- --- --- --- --- --- --- ---
+chr1 59699258 59699294 --- --- --- --- --- --- --- --- --- ---
+chr1 59898050 59898086 --- --- --- --- --- --- --- --- --- ---
+chr1 60028370 60028406 --- --- --- --- --- --- --- --- --- ---
+chr1 60369879 60369915 --- --- --- --- --- --- --- --- --- ---
+chr1 60744666 60744702 --- --- --- --- --- --- --- --- --- ---
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diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_features_per_peak1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_features_per_peak1.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,501 @@
+#peak.chr peak.start peak.end gene.id_1 strand_1 TSS_1 TES_1 dist_closest_1 dist_TSS_1 dist_TES_1 direction_1 overlap_gene_1 overlap_promoter_1 gene.id_2 strand_2 TSS_2 TES_2 dist_closest_2 dist_TSS_2 dist_TES_2 direction_2 overlap_gene_2 overlap_promoter_2 gene.id_3 strand_3 TSS_3 TES_3 dist_closest_3 dist_TSS_3 dist_TES_3 direction_3 overlap_gene_3 overlap_promoter_3 gene.id_4 strand_4 TSS_4 TES_4 dist_closest_4 dist_TSS_4 dist_TES_4 direction_4 overlap_gene_4 overlap_promoter_4
+chr1 3213477 3213513 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 3542857 3542893 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 3560979 3561015 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 3621547 3621583 AK149000 - 3648985 3638391 16808 27402 16808 D 0 0 Xkr4 - 3661579 3204562 0 39996 416985 . 1 0 . . . . . . . . . . . . . . . . . . . .
+chr1 4630453 4630489 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 5261737 5261773 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 5562257 5562293 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_features_per_peak3.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_features_per_peak3.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,2001 @@
+#peak.chr peak.start peak.end gene.id strand TSS TES dist_closest dist_TSS dist_TES direction overlap_gene overlap_promoter
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+chr1 3213477 3213513 --- --- --- --- --- --- --- --- --- ---
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+chr1 3560979 3561015 --- --- --- --- --- --- --- --- --- ---
+chr1 3621547 3621583 AK149000 - 3648985 3638391 16808 27402 16808 D 0 0
+chr1 3621547 3621583 Xkr4 - 3661579 3204562 0 39996 416985 . 1 0
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+chr1 13934524 13934560 --- --- --- --- --- --- --- --- --- ---
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+chr1 17334281 17334317 --- --- --- --- --- --- --- --- --- ---
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+chr1 17605285 17605321 --- --- --- --- --- --- --- --- --- ---
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+chr1 17922903 17922939 --- --- --- --- --- --- --- --- --- ---
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+chr1 17922903 17922939 --- --- --- --- --- --- --- --- --- ---
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+chr1 19213304 19213340 --- --- --- --- --- --- --- --- --- ---
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+chr1 31990075 31990111 --- --- --- --- --- --- --- --- --- ---
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diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_features_per_peak3.summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_features_per_peak3.summary Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,501 @@
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+chr1 154793310 154793346 --- --- --- --- --- --- --- --- --- ---
+chr1 154959021 154959057 --- --- --- --- --- --- --- --- --- ---
+chr1 155608292 155608328 --- --- --- --- --- --- --- --- --- ---
+chr1 155676641 155676677 --- --- --- --- --- --- --- --- --- ---
+chr1 155882149 155882185 --- --- --- --- --- --- --- --- --- ---
+chr1 156957961 156957997 --- --- --- --- --- --- --- --- --- ---
+chr1 157054389 157054425 --- --- --- --- --- --- --- --- --- ---
+chr1 157229460 157229496 --- --- --- --- --- --- --- --- --- ---
+chr1 157232537 157232573 --- --- --- --- --- --- --- --- --- ---
+chr1 157353367 157353403 --- --- --- --- --- --- --- --- --- ---
+chr1 157530064 157530100 --- --- --- --- --- --- --- --- --- ---
+chr1 157616665 157616701 --- --- --- --- --- --- --- --- --- ---
+chr1 157708175 157708211 --- --- --- --- --- --- --- --- --- ---
+chr1 157854160 157854196 --- --- --- --- --- --- --- --- --- ---
+chr1 157916567 157916603 --- --- --- --- --- --- --- --- --- ---
+chr1 157960555 157960591 --- --- --- --- --- --- --- --- --- ---
+chr1 158166030 158166066 --- --- --- --- --- --- --- --- --- ---
+chr1 158365460 158365496 --- --- --- --- --- --- --- --- --- ---
+chr1 158890212 158890248 --- --- --- --- --- --- --- --- --- ---
+chr1 159139993 159140029 --- --- --- --- --- --- --- --- --- ---
+chr1 159875548 159875584 --- --- --- --- --- --- --- --- --- ---
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_features_per_peak_compact.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_features_per_peak_compact.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,501 @@
+#chr start end gene.id_1 gene.id_2 gene.id_3 gene.id_4
+chr1 3213477 3213513 . . . .
+chr1 3542857 3542893 . . . .
+chr1 3560979 3561015 . . . .
+chr1 3621547 3621583 AK149000 Xkr4 . .
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+chr1 149151516 149151552 . . . .
+chr1 149373423 149373459 . . . .
+chr1 149547172 149547208 . . . .
+chr1 149930099 149930135 . . . .
+chr1 150523771 150523807 . . . .
+chr1 151852781 151852817 . . . .
+chr1 151941991 151942027 . . . .
+chr1 152055844 152055880 . . . .
+chr1 152768992 152769028 . . . .
+chr1 153117376 153117412 . . . .
+chr1 153562593 153562629 . . . .
+chr1 153617551 153617587 . . . .
+chr1 154259255 154259291 . . . .
+chr1 154305193 154305229 . . . .
+chr1 154793310 154793346 . . . .
+chr1 154959021 154959057 . . . .
+chr1 155608292 155608328 . . . .
+chr1 155676641 155676677 . . . .
+chr1 155882149 155882185 . . . .
+chr1 156957961 156957997 . . . .
+chr1 157054389 157054425 . . . .
+chr1 157229460 157229496 . . . .
+chr1 157232537 157232573 . . . .
+chr1 157353367 157353403 . . . .
+chr1 157530064 157530100 . . . .
+chr1 157616665 157616701 . . . .
+chr1 157708175 157708211 . . . .
+chr1 157854160 157854196 . . . .
+chr1 157916567 157916603 . . . .
+chr1 157960555 157960591 . . . .
+chr1 158166030 158166066 . . . .
+chr1 158365460 158365496 . . . .
+chr1 158890212 158890248 . . . .
+chr1 159139993 159140029 . . . .
+chr1 159875548 159875584 . . . .
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_features_per_summit.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_features_per_summit.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,501 @@
+#peak.chr peak.start peak.end gene.id_1 strand_1 TSS_1 TES_1 dist_closest_1 dist_TSS_1 dist_TES_1 direction_1 overlap_gene_1 overlap_promoter_1 gene.id_2 strand_2 TSS_2 TES_2 dist_closest_2 dist_TSS_2 dist_TES_2 direction_2 overlap_gene_2 overlap_promoter_2 gene.id_3 strand_3 TSS_3 TES_3 dist_closest_3 dist_TSS_3 dist_TES_3 direction_3 overlap_gene_3 overlap_promoter_3 gene.id_4 strand_4 TSS_4 TES_4 dist_closest_4 dist_TSS_4 dist_TES_4 direction_4 overlap_gene_4 overlap_promoter_4
+chr1 3213477 3213478 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 3542857 3542858 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 3560979 3560980 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 3621547 3621548 AK149000 - 3648985 3638391 16843 27437 16843 D 0 0 Xkr4 - 3661579 3204562 0 40031 416985 . 1 0 . . . . . . . . . . . . . . . . . . . .
+chr1 4630453 4630454 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 5261737 5261738 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 5562257 5562258 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 6926999 6927000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 7262846 7262847 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 7322487 7322488 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 7666187 7666188 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 7744070 7744071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 7969291 7969292 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 8421057 8421058 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 8679021 8679022 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 9359611 9359612 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 9415439 9415440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 9608130 9608131 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 9616803 9616804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 9897397 9897398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 10251725 10251726 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 10254195 10254196 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 10305254 10305255 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 10451286 10451287 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 11340573 11340574 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 11610483 11610484 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 11960381 11960382 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 11987310 11987311 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 12441678 12441679 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 12704380 12704381 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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+chr1 13934524 13934525 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 14479277 14479278 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 14755996 14755997 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 14848637 14848638 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 14967919 14967920 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 15097029 15097030 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 17128114 17128115 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 17160496 17160497 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 17334281 17334282 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 17605285 17605286 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 17922903 17922904 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 18681561 18681562 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 19213304 19213305 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 20317581 20317582 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 21466434 21466435 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 22074908 22074909 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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+chr1 23655828 23655829 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 24583893 24583894 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 24738828 24738829 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 24743796 24743797 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 25009857 25009858 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 25313509 25313510 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 26503310 26503311 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 27025916 27025917 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 27385857 27385858 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 27598627 27598628 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 27636264 27636265 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 27687524 27687525 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 28357424 28357425 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 29135026 29135027 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 29633575 29633576 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 29825940 29825941 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 30137793 30137794 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 30142141 30142142 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 30465754 30465755 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 30785908 30785909 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 31077695 31077696 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 31123645 31123646 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 31158742 31158743 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 31883682 31883683 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 31990075 31990076 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 33079863 33079864 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 33288587 33288588 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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+chr1 34588477 34588478 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 34633149 34633150 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 34749000 34749001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 34764419 34764420 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 35032286 35032287 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 35047073 35047074 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 35933401 35933402 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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+chr1 36742521 36742522 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 36859752 36859753 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 37388614 37388615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 37763263 37763264 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 37824535 37824536 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 37974386 37974387 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 37994576 37994577 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 38460553 38460554 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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+chr1 38832604 38832605 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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+chr1 39924300 39924301 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 40132160 40132161 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 40243823 40243824 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 40426457 40426458 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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+chr1 40785687 40785688 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 40953366 40953367 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 41021129 41021130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 41080072 41080073 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 41138125 41138126 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 41154639 41154640 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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+chr1 42463569 42463570 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 42518766 42518767 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 43783219 43783220 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 44575305 44575306 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 44600563 44600564 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 44982842 44982843 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 45305515 45305516 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 45339758 45339759 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 45422086 45422087 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 45824016 45824017 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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+chr1 51204752 51204753 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 51769267 51769268 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+chr1 52110888 52110889 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_peaks.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_peaks.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,500 @@
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+chr1 139093105 139093141
+chr1 139286502 139286538
+chr1 139448680 139448716
+chr1 139944056 139944092
+chr1 140207040 140207076
+chr1 141517452 141517488
+chr1 142087663 142087699
+chr1 142561476 142561512
+chr1 142732555 142732591
+chr1 142765329 142765365
+chr1 142811575 142811611
+chr1 142823331 142823367
+chr1 142985887 142985923
+chr1 143071919 143071955
+chr1 143137676 143137712
+chr1 143684082 143684118
+chr1 143803869 143803905
+chr1 143866547 143866583
+chr1 144585588 144585624
+chr1 145018626 145018662
+chr1 145169340 145169376
+chr1 145286043 145286079
+chr1 145743816 145743852
+chr1 145793073 145793109
+chr1 145943835 145943871
+chr1 145973347 145973383
+chr1 146233793 146233829
+chr1 146349912 146349948
+chr1 146992848 146992884
+chr1 147015972 147016008
+chr1 147919367 147919403
+chr1 148073000 148073036
+chr1 148184896 148184932
+chr1 148571263 148571299
+chr1 148727077 148727113
+chr1 148900032 148900068
+chr1 148988309 148988345
+chr1 149151516 149151552
+chr1 149373423 149373459
+chr1 149547172 149547208
+chr1 149930099 149930135
+chr1 150523771 150523807
+chr1 151852781 151852817
+chr1 151941991 151942027
+chr1 152055844 152055880
+chr1 152768992 152769028
+chr1 153117376 153117412
+chr1 153562593 153562629
+chr1 153617551 153617587
+chr1 154259255 154259291
+chr1 154305193 154305229
+chr1 154793310 154793346
+chr1 154959021 154959057
+chr1 155608292 155608328
+chr1 155676641 155676677
+chr1 155882149 155882185
+chr1 156957961 156957997
+chr1 157054389 157054425
+chr1 157229460 157229496
+chr1 157232537 157232573
+chr1 157353367 157353403
+chr1 157530064 157530100
+chr1 157616665 157616701
+chr1 157708175 157708211
+chr1 157854160 157854196
+chr1 157916567 157916603
+chr1 157960555 157960591
+chr1 158166030 158166066
+chr1 158365460 158365496
+chr1 158890212 158890248
+chr1 159139993 159140029
+chr1 159875548 159875584
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_peaks.xls
Binary file test-data/mm9_peaks.xls has changed
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_peaks1.xlsx
Binary file test-data/mm9_peaks1.xlsx has changed
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_peaks3.xlsx
Binary file test-data/mm9_peaks3.xlsx has changed
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_peaks_compact.xls
Binary file test-data/mm9_peaks_compact.xls has changed
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_peaks_per_feature.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_peaks_per_feature.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,10 @@
+#gene.id gene.chr gene.start gene.end gene.strand peak.chr peak.start peak.end order dist_closest dist_TSS dist_TES
+Xkr4 chr1 3204562 3661579 - chr1 3621547 3621583 1 of 1 0 39996 416985
+AK149000 chr1 3638391 3648985 - chr1 3621547 3621583 1 of 1 16808 27402 16808
+Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- ---
+Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- ---
+Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- ---
+Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- ---
+Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- ---
+Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- ---
+Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- ---
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_peaks_per_feature1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_peaks_per_feature1.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,10 @@
+#gene.id gene.chr gene.start gene.end gene.strand chr_1 start_1 end_1 dist_closest_1 dist_TSS_1 direction_1 in_the_gene_1 chr_2 start_2 end_2 dist_closest_2 dist_TSS_2 direction_2 in_the_gene_2 chr_3 start_3 end_3 dist_closest_3 dist_TSS_3 direction_3 in_the_gene_3 chr_4 start_4 end_4 dist_closest_4 dist_TSS_4 direction_4 in_the_gene_4
+Xkr4 chr1 3204562 3661579 - chr1 3621547 3621583 0 39996 . YES . . . . . . . . . . . . . . . . . . . . .
+AK149000 chr1 3638391 3648985 - chr1 3621547 3621583 16808 27402 U NO . . . . . . . . . . . . . . . . . . . . .
+Rp1 chr1 4333587 4350395 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Sox17 chr1 4481008 4486494 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Mrpl15 chr1 4763278 4775807 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Lypla1 chr1 4797973 4836816 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Tcea1 chr1 4847774 4887990 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Rgs20 chr1 4899656 5060366 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Atp6v1h chr1 5073253 5152630 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_peaks_per_feature3.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_peaks_per_feature3.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,37 @@
+#gene.id gene.chr gene.start gene.end gene.strand chr start end dist_closest dist_TSS direction in_the_gene
+Xkr4 chr1 3204562 3661579 - chr1 3621547 3621583 0 39996 . YES
+Xkr4 chr1 3204562 3661579 - --- --- --- --- --- --- ---
+Xkr4 chr1 3204562 3661579 - --- --- --- --- --- --- ---
+Xkr4 chr1 3204562 3661579 - --- --- --- --- --- --- ---
+AK149000 chr1 3638391 3648985 - chr1 3621547 3621583 16808 27402 U NO
+AK149000 chr1 3638391 3648985 - --- --- --- --- --- --- ---
+AK149000 chr1 3638391 3648985 - --- --- --- --- --- --- ---
+AK149000 chr1 3638391 3648985 - --- --- --- --- --- --- ---
+Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- ---
+Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- ---
+Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- ---
+Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- ---
+Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- ---
+Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- ---
+Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- ---
+Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- ---
+Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- ---
+Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- ---
+Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- ---
+Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- ---
+Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- ---
+Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- ---
+Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- ---
+Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- ---
+Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- ---
+Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- ---
+Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- ---
+Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- ---
+Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- ---
+Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- ---
+Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- ---
+Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- ---
+Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- ---
+Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- ---
+Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- ---
+Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- ---
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_peaks_per_feature3.summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_peaks_per_feature3.summary Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,10 @@
+#gene.id gene.chr gene.start gene.end gene.strand chr start end dist_closest dist_TSS direction in_the_gene
+Xkr4 chr1 3204562 3661579 - chr1 3621547 3621583 0 39996 . YES
+AK149000 chr1 3638391 3648985 - chr1 3621547 3621583 16808 27402 U NO
+Rp1 chr1 4333587 4350395 - --- --- --- --- --- --- ---
+Sox17 chr1 4481008 4486494 - --- --- --- --- --- --- ---
+Mrpl15 chr1 4763278 4775807 - --- --- --- --- --- --- ---
+Lypla1 chr1 4797973 4836816 + --- --- --- --- --- --- ---
+Tcea1 chr1 4847774 4887990 + --- --- --- --- --- --- ---
+Rgs20 chr1 4899656 5060366 - --- --- --- --- --- --- ---
+Atp6v1h chr1 5073253 5152630 + --- --- --- --- --- --- ---
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_peaks_per_feature_compact.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_peaks_per_feature_compact.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,10 @@
+#gene.id chr_1 start_1 end_1 dist_closest_1 direction_1 chr_2 start_2 end_2 dist_closest_2 direction_2 chr_3 start_3 end_3 dist_closest_3 direction_3 chr_4 start_4 end_4 dist_closest_4 direction_4
+Xkr4 chr1 3621547 3621583 0 . . . . . . . . . . . . . . . .
+AK149000 chr1 3621547 3621583 16808 U . . . . . . . . . . . . . . .
+Rp1 . . . . . . . . . . . . . . . . . . . .
+Sox17 . . . . . . . . . . . . . . . . . . . .
+Mrpl15 . . . . . . . . . . . . . . . . . . . .
+Lypla1 . . . . . . . . . . . . . . . . . . . .
+Tcea1 . . . . . . . . . . . . . . . . . . . .
+Rgs20 . . . . . . . . . . . . . . . . . . . .
+Atp6v1h . . . . . . . . . . . . . . . . . . . .
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_summits.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_summits.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,500 @@
+chr1 3213477 3213478
+chr1 3542857 3542858
+chr1 3560979 3560980
+chr1 3621547 3621548
+chr1 4630453 4630454
+chr1 5261737 5261738
+chr1 5562257 5562258
+chr1 6926999 6927000
+chr1 7262846 7262847
+chr1 7322487 7322488
+chr1 7666187 7666188
+chr1 7744070 7744071
+chr1 7969291 7969292
+chr1 8421057 8421058
+chr1 8679021 8679022
+chr1 9359611 9359612
+chr1 9415439 9415440
+chr1 9608130 9608131
+chr1 9616803 9616804
+chr1 9897397 9897398
+chr1 10251725 10251726
+chr1 10254195 10254196
+chr1 10305254 10305255
+chr1 10451286 10451287
+chr1 11340573 11340574
+chr1 11610483 11610484
+chr1 11960381 11960382
+chr1 11987310 11987311
+chr1 12441678 12441679
+chr1 12704380 12704381
+chr1 12871650 12871651
+chr1 13179280 13179281
+chr1 13934524 13934525
+chr1 14479277 14479278
+chr1 14755996 14755997
+chr1 14848637 14848638
+chr1 14967919 14967920
+chr1 15097029 15097030
+chr1 17128114 17128115
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+chr1 36135485 36135486
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+chr1 41021129 41021130
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+chr1 117105699 117105700
+chr1 117651574 117651575
+chr1 117666069 117666070
+chr1 118378031 118378032
+chr1 119053534 119053535
+chr1 119113385 119113386
+chr1 119174525 119174526
+chr1 119503762 119503763
+chr1 119527726 119527727
+chr1 119948214 119948215
+chr1 120267925 120267926
+chr1 120380981 120380982
+chr1 120465310 120465311
+chr1 120797706 120797707
+chr1 121041195 121041196
+chr1 121094948 121094949
+chr1 121167893 121167894
+chr1 121340746 121340747
+chr1 121587267 121587268
+chr1 121681260 121681261
+chr1 121816202 121816203
+chr1 123026661 123026662
+chr1 123170986 123170987
+chr1 123685384 123685385
+chr1 123835178 123835179
+chr1 123920817 123920818
+chr1 123949970 123949971
+chr1 124461424 124461425
+chr1 125400371 125400372
+chr1 126171930 126171931
+chr1 126179030 126179031
+chr1 126687579 126687580
+chr1 126712327 126712328
+chr1 126783497 126783498
+chr1 126787012 126787013
+chr1 126963082 126963083
+chr1 127190153 127190154
+chr1 127228396 127228397
+chr1 127507342 127507343
+chr1 127703188 127703189
+chr1 127735504 127735505
+chr1 128049231 128049232
+chr1 128388917 128388918
+chr1 128791747 128791748
+chr1 129571914 129571915
+chr1 129582844 129582845
+chr1 130923911 130923912
+chr1 131245002 131245003
+chr1 131624212 131624213
+chr1 131653028 131653029
+chr1 131673494 131673495
+chr1 131762457 131762458
+chr1 132812150 132812151
+chr1 133122490 133122491
+chr1 133337646 133337647
+chr1 134107973 134107974
+chr1 134516117 134516118
+chr1 134650852 134650853
+chr1 135304596 135304597
+chr1 135346221 135346222
+chr1 135595351 135595352
+chr1 135645557 135645558
+chr1 135794196 135794197
+chr1 135833373 135833374
+chr1 136109219 136109220
+chr1 136151385 136151386
+chr1 136219228 136219229
+chr1 136276302 136276303
+chr1 136409892 136409893
+chr1 136846450 136846451
+chr1 137021089 137021090
+chr1 137057829 137057830
+chr1 137256872 137256873
+chr1 137292997 137292998
+chr1 137340715 137340716
+chr1 137563013 137563014
+chr1 138237818 138237819
+chr1 138288739 138288740
+chr1 138701415 138701416
+chr1 138883160 138883161
+chr1 139093105 139093106
+chr1 139286502 139286503
+chr1 139448680 139448681
+chr1 139944056 139944057
+chr1 140207040 140207041
+chr1 141517452 141517453
+chr1 142087663 142087664
+chr1 142561476 142561477
+chr1 142732555 142732556
+chr1 142765329 142765330
+chr1 142811575 142811576
+chr1 142823331 142823332
+chr1 142985887 142985888
+chr1 143071919 143071920
+chr1 143137676 143137677
+chr1 143684082 143684083
+chr1 143803869 143803870
+chr1 143866547 143866548
+chr1 144585588 144585589
+chr1 145018626 145018627
+chr1 145169340 145169341
+chr1 145286043 145286044
+chr1 145743816 145743817
+chr1 145793073 145793074
+chr1 145943835 145943836
+chr1 145973347 145973348
+chr1 146233793 146233794
+chr1 146349912 146349913
+chr1 146992848 146992849
+chr1 147015972 147015973
+chr1 147919367 147919368
+chr1 148073000 148073001
+chr1 148184896 148184897
+chr1 148571263 148571264
+chr1 148727077 148727078
+chr1 148900032 148900033
+chr1 148988309 148988310
+chr1 149151516 149151517
+chr1 149373423 149373424
+chr1 149547172 149547173
+chr1 149930099 149930100
+chr1 150523771 150523772
+chr1 151852781 151852782
+chr1 151941991 151941992
+chr1 152055844 152055845
+chr1 152768992 152768993
+chr1 153117376 153117377
+chr1 153562593 153562594
+chr1 153617551 153617552
+chr1 154259255 154259256
+chr1 154305193 154305194
+chr1 154793310 154793311
+chr1 154959021 154959022
+chr1 155608292 155608293
+chr1 155676641 155676642
+chr1 155882149 155882150
+chr1 156957961 156957962
+chr1 157054389 157054390
+chr1 157229460 157229461
+chr1 157232537 157232538
+chr1 157353367 157353368
+chr1 157530064 157530065
+chr1 157616665 157616666
+chr1 157708175 157708176
+chr1 157854160 157854161
+chr1 157916567 157916568
+chr1 157960555 157960556
+chr1 158166030 158166031
+chr1 158365460 158365461
+chr1 158890212 158890213
+chr1 159139993 159139994
+chr1 159875548 159875549
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_summits.xlsx
Binary file test-data/mm9_summits.xlsx has changed
diff -r 000000000000 -r 0abe6bac47a6 test-data/mm9_summits_per_feature.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_summits_per_feature.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,10 @@
+#gene.id gene.chr gene.start gene.end gene.strand chr_1 start_1 end_1 dist_closest_1 dist_TSS_1 direction_1 in_the_gene_1 chr_2 start_2 end_2 dist_closest_2 dist_TSS_2 direction_2 in_the_gene_2 chr_3 start_3 end_3 dist_closest_3 dist_TSS_3 direction_3 in_the_gene_3 chr_4 start_4 end_4 dist_closest_4 dist_TSS_4 direction_4 in_the_gene_4
+Xkr4 chr1 3204562 3661579 - chr1 3621547 3621548 0 40031 . YES . . . . . . . . . . . . . . . . . . . . .
+AK149000 chr1 3638391 3648985 - chr1 3621547 3621548 16843 27437 U NO . . . . . . . . . . . . . . . . . . . . .
+Rp1 chr1 4333587 4350395 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Sox17 chr1 4481008 4486494 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Mrpl15 chr1 4763278 4775807 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Lypla1 chr1 4797973 4836816 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Tcea1 chr1 4847774 4887990 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Rgs20 chr1 4899656 5060366 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+Atp6v1h chr1 5073253 5152630 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
diff -r 000000000000 -r 0abe6bac47a6 test-data/peaks.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peaks.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,70 @@
+#peak s e
+chr1 10617233 10617437
+chr1 108747519 108747791
+chr1 120760212 120760461
+chr1 132950929 132951247
+chr1 133114860 133115015
+chr1 135582677 135582828
+chr1 135851853 135852218
+chr1 136956468 136956598
+chr1 13829227 13829564
+chr1 138437726 138437860
+chr1 140381656 140381785
+chr1 145591041 145591176
+chr1 154971572 154971673
+chr1 155123313 155123435
+chr1 158510523 158510813
+chr1 158537267 158537411
+chr1 158580638 158580759
+chr1 158835251 158835391
+chr1 159240736 159240866
+chr1 163827897 163828062
+chr1 164215623 164215935
+chr1 167222964 167223261
+chr1 167906284 167906554
+chr1 170255081 170255260
+chr1 17030405 17030545
+chr1 172620779 172620912
+chr1 172620917 172621080
+chr1 174376470 174376659
+chr1 181061299 181061446
+chr1 182479646 182479905
+chr1 185854947 185855105
+chr1 194258648 194259032
+chr1 194645118 194645475
+chr1 194957396 194957723
+chr1 195324443 195324741
+chr1 195330701 195330930
+chr1 195338316 195338616
+chr1 195342728 195342985
+chr1 195384767 195385195
+chr1 197057796 197057843
+chr1 24609562 24609623
+chr1 24609923 24609992
+chr1 24730996 24731077
+chr1 26734195 26734485
+chr1 34206924 34207100
+chr1 36106813 36107058
+chr1 39492140 39492513
+chr1 40325917 40326123
+chr1 44195449 44195639
+chr1 52625416 52625560
+chr1 54631692 54631815
+chr1 55283572 55283675
+chr1 63664888 63665018
+chr1 72769824 72770056
+chr1 72770058 72770226
+chr1 72815517 72815742
+chr1 75481920 75482054
+chr1 77457642 77457791
+chr1 78630893 78631160
+chr1 88408969 88409267
+chr1 89989553 89989714
+chr1 90412932 90413132
+chr1 90592499 90592629
+chr1 91496003 91496145
+chr1 91496155 91496319
+chr1 92070253 92070431
+chr1 95186508 95186637
+chr1 9619046 9619167
+chr1 9619175 9619382
diff -r 000000000000 -r 0abe6bac47a6 test-data/peaks1.xlsx
Binary file test-data/peaks1.xlsx has changed
diff -r 000000000000 -r 0abe6bac47a6 test-data/peaks2.xlsx
Binary file test-data/peaks2.xlsx has changed
diff -r 000000000000 -r 0abe6bac47a6 test-data/peaks3.xlsx
Binary file test-data/peaks3.xlsx has changed
diff -r 000000000000 -r 0abe6bac47a6 test-data/peaks4.xlsx
Binary file test-data/peaks4.xlsx has changed
diff -r 000000000000 -r 0abe6bac47a6 test-data/peaks_per_feature1.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peaks_per_feature1.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,957 @@
+#gene.id gene.chr gene.start gene.end gene.strand chr_1 start_1 end_1 dist_closest_1 dist_TSS_1 direction_1 in_the_gene_1 chr_2 start_2 end_2 dist_closest_2 dist_TSS_2 direction_2 in_the_gene_2 chr_3 start_3 end_3 dist_closest_3 dist_TSS_3 direction_3 in_the_gene_3 chr_4 start_4 end_4 dist_closest_4 dist_TSS_4 direction_4 in_the_gene_4
+AF064749_Col6a3 chr1 92566771 92800755 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK015559_4930472D16Rik chr1 25020851 25021989 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK030377_A330023F24Rik chr1 196781953 196826186 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK080193_A530079E22Rik chr1 89401837 89403491 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK082264_C230030N03Rik chr1 34735043 34781084 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC006931_AI597479 chr1 43153807 43172843 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC021773_Glb1l chr1 75193364 75207353 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC023951_D1Ertd622e chr1 99540054 99558631 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC028767_3110009E18Rik chr1 122017764 122114603 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC031781_BC031781 chr1 182781250 182798240 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC034187_BC035947 chr1 78493611 78497758 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC043098_Fam168b chr1 34870072 34917183 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC049091_D1Bwg0212e chr1 39592545 39603734 + chr1 39492140 39492513 100032 100032 D NO . . . . . . . . . . . . . . . . . . . . .
+BC049713_Ankrd45 chr1 163072817 163099826 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC050813_4921511C04Rik chr1 37157481 37244861 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC051128_4921521F21Rik chr1 65059273 65079312 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC052693_2810422O20Rik chr1 165924541 165927371 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC052931_A630001G21Rik chr1 87601462 87674840 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC053100_5730559C18Rik chr1 138110108 138130841 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC054802_9630058J23Rik chr1 181476521 181558044 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC055845_2810025M15Rik chr1 159342483 159350353 + chr1 159240736 159240866 101617 101617 D NO . . . . . . . . . . . . . . . . . . . . .
+BC055955_A130010J15Rik chr1 194999663 195004015 + chr1 194957396 194957723 41940 41940 D NO . . . . . . . . . . . . . . . . . . . . .
+BC057872_Rab3gap2 chr1 187028006 187110623 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC058417_2610017I09Rik chr1 42648822 42751667 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC059254_Phlpp chr1 108042052 108306367 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC070435_Fam123c chr1 34620070 34671545 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC070446_Fam135a chr1 24017617 24107170 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC071241_9430016H08Rik chr1 57463192 57497936 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC072639_2010300C02Rik chr1 37646877 37776659 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC080290_5033414K04Rik chr1 84032539 84360735 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC082310_9430031J16Rik chr1 81073525 81338329 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC089525_2310007B03Rik chr1 95047933 95063386 - chr1 95186508 95186637 123122 123122 D NO . . . . . . . . . . . . . . . . . . . . .
+BC089561_Cep350 chr1 157692096 157820375 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC147491_A230074B11Rik chr1 37083441 37133840 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC147657_9630028B13Rik chr1 187253234 187265698 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000027997_Rgs5 chr1 171625108 171625913 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000051203_1700001G17Rik chr1 33726669 33727551 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000054333_A130050O07Rik chr1 139823828 139826840 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000056879_C230029F24Rik chr1 49301475 49397265 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000057543_A730013G03Rik chr1 194659323 194661397 - chr1 194645118 194645475 13848 15922 U NO . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000062637_4930470H14Rik chr1 175156866 175201240 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000070048_ENSMUSG00000056128 chr1 92571736 92576368 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000070987_EG433384 chr1 183781705 183783320 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000072395_Olfr1406 chr1 175113651 175120746 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000094288_Wdr64 chr1 177654798 177798070 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000094950_Pgap1 chr1 54529849 54614539 - chr1 54631692 54631815 17153 17153 D NO . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000097776_Cnnm3 chr1 36567938 36585164 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+EU429481_Igfn1 chr1 137825893 137890307 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+FJ024495_Ildr2 chr1 168236882 168239692 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+FJ210934_Unc80 chr1 66514856 66556109 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001001565_Chpf chr1 75470923 75476437 - chr1 75481920 75482054 5483 5483 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_001001809_Olfr218 chr1 175130421 175134469 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001001883_Hecw2 chr1 53867026 54252002 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001003917_Atg9a chr1 75177439 75189181 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001004173_Sgpp2 chr1 78306692 78416864 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001005423_Mreg chr1 72170192 72258895 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001005507_Smg7 chr1 154684125 154750410 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001005508_Arhgap30 chr1 173319072 173340822 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001005520_Olfr244 chr1 176032571 176067605 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001008419_Aox3l1 chr1 58335180 58437083 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001008426_EG433365 chr1 155721475 155724001 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001008533_Adora1 chr1 136095799 136181661 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001009940_Il19 chr1 132786042 132915234 - chr1 132950929 132951247 35695 35695 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_001011525_Olfr1415 chr1 94376258 94381054 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001011525_Olfr1415 chr1 94407669 94418761 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001011684_Nms chr1 38995917 39007113 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001011873_Xkr9 chr1 13658862 13691794 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001011874_Xkr4 chr1 3203722 3713108 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001012330_Zfp238 chr1 179359958 179380892 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001013374_Lman2l chr1 36362897 36502078 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001013382_Lrrc52 chr1 169375806 169397136 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001013771_Gm973 chr1 59573136 59693241 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001013779_Aim2 chr1 175385835 175396165 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001014974_Ttll4 chr1 74708314 74748400 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001024721_BC094916 chr1 175451304 175466101 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001024945_Qsox1 chr1 157625296 157670499 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001025156_Ccdc93 chr1 123208865 123403037 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001025565_Lhx9 chr1 140694768 140740509 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001025602_Il1rl1 chr1 40462708 40522260 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001029984_Fcrlb chr1 172836813 172843072 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001037170_Tomm40l chr1 173147934 173152645 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001037725_Fam117b chr1 59937517 60042190 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001037918_Lipt1 chr1 37928603 37934232 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001037999_Dbi chr1 122009883 122046068 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001038592_Glrx2 chr1 145585774 145608282 + chr1 145591041 145591176 0 5267 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_001038619_Dnm3 chr1 163902671 164408155 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039126_Asb1 chr1 93437143 93461729 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039472_Kif21b chr1 138027986 138074578 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039475_Slco6b1 chr1 98802763 98894139 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039482_Klhl20 chr1 163018528 163061699 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039483_Tmco1 chr1 169238419 169279112 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039484_Kcnj10 chr1 174258852 174304216 + chr1 174376470 174376659 72254 117618 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_001039493_Plekhm3 chr1 64832557 65032270 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039495_Ccdc108 chr1 74947239 74982168 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039509_Pnkd chr1 74331504 74400245 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039710_Coq10b chr1 55101051 55129538 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039934_Mtap2 chr1 66187374 66489157 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001042634_Clk1 chr1 58467034 58480936 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001045481_Ifi203 chr1 175804708 175928457 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001077189_Fcgr2b chr1 172890316 172916060 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001077353_Gsta3 chr1 21230690 21255722 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001077403_Nrp2 chr1 62724499 63100251 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081023_Cacna1s chr1 137949297 138016348 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081078_Lct chr1 130174327 130224881 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081079_Ogfrl1 chr1 23278472 23451348 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081259_Mfsd7b chr1 192825304 192850534 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081275_1700009P17Rik chr1 173032694 173057075 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081361_Mosc1 chr1 186610666 186635172 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081756_E030049G20Rik chr1 128277776 128727190 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001082573_Crygc chr1 65118108 65146863 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001083897_Mpzl1 chr1 167522314 167564669 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001085409_Steap3 chr1 122037552 122169282 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001099637_Cep170 chr1 178663793 178744307 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001103182_Lin9 chr1 182572002 182620816 + chr1 182479646 182479905 92097 92097 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_001105667_Dtymk chr1 95689006 95698492 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001110783_Ank1 chr1 77759424 77766452 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001110831_Dnpep chr1 75304471 75314673 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001111059_Cd34 chr1 196683888 196826273 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001111279_Wdfy1 chr1 79689958 79772698 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001111314_Ngef chr1 89373415 89470499 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001111316_Ptprc chr1 139959456 140088994 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001111320_Idh1 chr1 65185668 65233033 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001113394_Cd247 chr1 167711216 167807397 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001122685_Rhbdd1 chr1 82313047 82441937 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001126046_Fam178b chr1 36619544 36740008 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001128605_Psen2 chr1 182157140 182247499 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001128609_Dedd chr1 173258959 173273620 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001130174_Tnnt2 chr1 137732931 137748838 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001134829_Lpgat1 chr1 193521144 193605705 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001136070_Lgtn chr1 133049773 133084235 + chr1 133114860 133115015 30625 65087 U NO chr1 132950929 132951247 98526 98526 D NO . . . . . . . . . . . . . .
+NM_001142647_Tmem194b chr1 52687569 52708760 + chr1 52625416 52625560 62009 62009 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_001159649_Lax1 chr1 135575626 135586665 - chr1 135582677 135582828 0 3837 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_001159719_Sept2 chr1 95375046 95406820 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001159730_Pdc chr1 152154402 152181077 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007381_Acadl chr1 66861363 66909886 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007415_Parp1 chr1 182499033 182531385 + chr1 182479646 182479905 19128 19128 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_007422_Adss chr1 179693113 179888685 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007432_Akp3 chr1 89021583 89042994 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007433_Akp5 chr1 88983274 88986861 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007453_Prdx6 chr1 163170243 163210238 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007463_Speg chr1 75371872 75428879 + chr1 75481920 75482054 53041 110048 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_007495_Astn1 chr1 160292424 160626748 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007498_Atf3 chr1 192994178 193057173 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007525_Bard1 chr1 71076934 71149526 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007561_Bmpr2 chr1 59820296 59927706 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007570_Btg2 chr1 135971251 135991759 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007576_C4bp chr1 132531357 132558199 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007642_Cd28 chr1 60763315 60830749 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007649_Cd48 chr1 173603288 173635385 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007685_Cfc1 chr1 34592493 34601156 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007695_Chi3l1 chr1 136069840 136086738 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007722_Cxcr7 chr1 92100063 92112863 + chr1 92070253 92070431 29632 29632 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_007733_Col19a1 chr1 24258667 24602262 - chr1 24609562 24609623 7300 7300 D NO chr1 24609923 24609992 7661 7661 D NO chr1 24730996 24731077 128734 128734 D NO . . . . . . .
+NM_007734_Col4a3 chr1 82583506 82718629 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007735_Col4a4 chr1 82438140 82584744 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007737_Col5a2 chr1 45431177 45560226 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007740_Col9a1 chr1 24164692 24268636 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007758_Cr2 chr1 196963005 197003002 - chr1 197057796 197057843 54794 54794 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_007768_Crp chr1 174620782 174763152 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007774_Cryga chr1 65146986 65150012 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007776_Crygd chr1 65108417 65110024 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007777_Cryge chr1 65095133 65097767 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007791_Csrp1 chr1 137526251 137648807 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007799_Ctse chr1 133534879 133572077 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007827_Daf2 chr1 132285116 132319576 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007842_Dhx9 chr1 155302618 155334755 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007853_Degs1 chr1 184205901 184212915 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007921_Elf3 chr1 137149649 137155139 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007923_Elk4 chr1 133904204 133929189 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007936_Epha4 chr1 77280640 77511653 - chr1 77457642 77457791 0 53862 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_007955_Ptprv chr1 137004306 137029151 - chr1 136956468 136956598 47708 72553 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_007976_F5 chr1 166081877 166150388 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008030_Fmo3 chr1 164883934 164914811 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008057_Fzd7 chr1 59538966 59546428 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008059_G0s2 chr1 195098362 195108977 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008131_Glul chr1 155746721 155757023 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008132_Glrp1 chr1 90396446 90406631 - chr1 90412932 90413132 6301 6301 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_008209_Mr1 chr1 156951231 157006024 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008210_H3f3a chr1 182694052 182744054 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008250_Hlx chr1 186542564 186592227 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008288_Hsd11b1 chr1 195047814 195090228 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008299_Dnajb3 chr1 90101307 90102337 - chr1 89989553 89989714 111593 112623 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_008311_Htr2b chr1 87995611 88008576 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008327_Ifi202b chr1 175892699 175912872 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008329_Ifi204 chr1 175677424 175929523 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008342_Igfbp2 chr1 72840313 72899038 + chr1 72815517 72815742 24571 24571 D NO chr1 72770058 72770226 70087 70087 D NO chr1 72769824 72770056 70257 70257 D NO . . . . . . .
+NM_008362_Il1r1 chr1 40274145 40373439 + chr1 40325917 40326123 0 51772 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_008365_Il18r1 chr1 40522407 40557703 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008384_Inpp1 chr1 52826936 52890006 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008429_Kcnj9 chr1 174250632 174259434 - chr1 174376470 174376659 117036 117036 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_008440_Kif1a chr1 94912041 94998420 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008484_Lamb3 chr1 195033913 195170047 + chr1 194957396 194957723 76190 76190 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_008485_Lamc2 chr1 154969890 155033557 - chr1 154971572 154971673 0 61884 . YES chr1 155123313 155123435 89756 89756 D NO . . . . . . . . . . . . . .
+NM_008510_Xcl1 chr1 166861801 166916999 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008515_Lrrfip1 chr1 92895314 93025509 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008534_Ly9 chr1 173518153 173537531 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008551_Mapkapk2 chr1 132950274 133013820 - chr1 132950929 132951247 0 62573 . YES chr1 133114860 133115015 101040 101040 D NO . . . . . . . . . . . . . .
+NM_008563_Mcm3 chr1 20792654 20810343 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008567_Mcm6 chr1 130228167 130256262 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008575_Mdm4 chr1 134877138 134927144 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008623_Mpz chr1 173081953 173091254 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008651_Mybl1 chr1 9635825 9690280 - chr1 9619175 9619382 16443 70898 U NO chr1 9619046 9619167 16658 71113 U NO . . . . . . . . . . . . . .
+NM_008667_Nab1 chr1 52487127 52611216 - chr1 52625416 52625560 14200 14200 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_008678_Ncoa2 chr1 13129206 13399268 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008696_Map4k4 chr1 39958025 40102235 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008719_Npas2 chr1 39250631 39420071 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008763_Olfr16 chr1 174886928 174887857 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008765_Orc2l chr1 58519275 58561933 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008781_Pax3 chr1 78047196 78193701 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008795_Pctk3 chr1 133972174 134036519 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008798_Pdcd1 chr1 95931620 95977526 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008801_Pde6d chr1 88427331 88479102 - chr1 88408969 88409267 18064 69835 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_008825_Pfkfb2 chr1 132566787 132625820 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008866_Lypla1 chr1 4797815 4844373 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008869_Pla2g4a chr1 151661289 151808414 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008882_Plxna2 chr1 196411150 196654445 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008900_Pou3f3 chr1 42662066 42757055 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008911_Ppox chr1 173200042 173211335 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008922_Prim2 chr1 33510658 33727287 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008937_Prox1 chr1 191943166 191999411 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008976_Ptpn14 chr1 191512039 191694746 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008985_Ptprn chr1 75243625 75261057 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008998_Rab17 chr1 92842177 92905581 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008999_Rab23 chr1 33776747 33799402 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009049_Resp18 chr1 75268774 75274970 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009061_Rgs2 chr1 145846468 145858945 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009062_Rgs4 chr1 171671620 171743114 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009063_Rgs5 chr1 171585632 171625107 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009107_Rxrg chr1 169399669 169569753 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009118_Sag chr1 89700275 89741733 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009126_Serpinb3a chr1 108942184 108948902 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009129_Scg2 chr1 79431244 79436675 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009183_St8sia4 chr1 97484259 97672426 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009190_Vps4b chr1 108665873 108739123 - chr1 108747519 108747791 8396 8396 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_009208_Slc4a3 chr1 75539833 75564973 + chr1 75481920 75482054 57779 57779 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_009230_Soat1 chr1 158354679 158417632 - chr1 158510523 158510813 92891 92891 D NO chr1 158537267 158537411 119635 119635 D NO . . . . . . . . . . . . . .
+NM_009255_Serpine2 chr1 79778648 79891246 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009257_Serpinb5 chr1 108757652 108779925 + chr1 108747519 108747791 9861 9861 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_009283_Stat1 chr1 51740305 52218707 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009307_Syt2 chr1 136543209 136659150 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009334_Tcfap2b chr1 19198995 19228906 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009352_Terf1 chr1 15785995 15845901 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009355_Tesp1 chr1 34554997 34559905 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009356_Tesp2 chr1 34594321 34617749 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009367_Tgfb2 chr1 188337162 188544530 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009399_Tnfrsf11a chr1 107677300 107859295 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009407_Tnp1 chr1 73061657 73062512 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009418_Tpp2 chr1 43936027 44065003 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009447_Tuba4a chr1 75210818 75219831 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009452_Tnfsf4 chr1 163212600 163374314 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009460_Sumo1 chr1 59643412 59727658 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009480_Usf1 chr1 173341335 173348954 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009509_Vil1 chr1 74455970 74485488 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009518_Wnt10a chr1 74838090 74898253 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009526_Wnt6 chr1 74818493 74831875 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009533_Xrcc5 chr1 72354001 72453365 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009539_Zap70 chr1 36818663 36839663 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009579_Slc30a1 chr1 193730666 193737101 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009581_Zp3r chr1 132473290 132526179 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009604_Chrng chr1 89102267 89109269 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009676_Aox1 chr1 58086687 58165423 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009721_Atp1b1 chr1 166367243 166524675 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009741_Bcl2 chr1 108362593 108614036 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009782_Cacna1e chr1 156242220 156916799 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009786_Cacybp chr1 162132500 162143003 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009791_Aspm chr1 141351360 141393207 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009794_Capn2 chr1 184394108 184479307 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009803_Nr1i3 chr1 173122612 173149661 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009812_Casp8 chr1 58818409 58904327 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009813_Casq1 chr1 174140028 174150006 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009826_Rb1cc1 chr1 6196277 6266709 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009843_Ctla4 chr1 60943864 61098205 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009872_Cdk5r2 chr1 74901511 74904288 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009909_Il8rb chr1 74200075 74207820 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009911_Cxcr4 chr1 130436268 130609324 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009918_Cnga3 chr1 37275192 37321882 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009930_Col3a1 chr1 45368295 45413500 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009938_Copa chr1 174012565 174052450 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010016_Cd55 chr1 132326379 132359520 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010043_Des chr1 75356887 75365134 + chr1 75481920 75482054 116786 125033 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_010045_Darc chr1 175234342 175263520 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010094_Lefty1 chr1 182865132 182868532 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010098_Opn3 chr1 177592560 177622774 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010133_En1 chr1 122494080 122540975 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010135_Enah chr1 183776371 183949877 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010145_Ephx1 chr1 182919689 182951015 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010164_Eya1 chr1 14117632 14318907 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010177_Fasl chr1 163710820 163718844 - chr1 163827897 163828062 109053 109053 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_010184_Fcer1a chr1 175148098 175157377 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010185_Fcer1g chr1 173159708 173164476 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010188_Fcgr3 chr1 172916162 173015807 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010209_Fh1 chr1 177427308 177555746 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010212_Fhl2 chr1 43179941 43255166 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010231_Fmo1 chr1 164744557 164796721 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010233_Fn1 chr1 71632113 71736637 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010262_Gbx2 chr1 91824531 91831059 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010267_Gdap1 chr1 17135463 17385513 + chr1 17030405 17030545 104918 104918 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_010341_Nmur1 chr1 88282479 88297441 - chr1 88408969 88409267 111528 111528 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_010472_Agfg1 chr1 82836048 82918151 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010476_Hsd17b7 chr1 171879671 171899542 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010483_Htr5b chr1 123406263 123425032 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010500_Ier5 chr1 156943491 156946949 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010518_Igfbp5 chr1 72904507 72921468 - chr1 72815517 72815742 88765 105726 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_010544_Ihh chr1 74991633 75093213 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010548_Il10 chr1 132916424 132921547 + chr1 132950929 132951247 29382 34505 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_010552_Il17a chr1 20660053 20766059 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010553_Il18rap chr1 40572207 40606867 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010555_Il1r2 chr1 40130058 40182052 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010564_Inha chr1 75503647 75506924 + chr1 75481920 75482054 21593 21593 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_010566_Inpp5d chr1 89504177 89645401 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010570_Irs1 chr1 82229682 82233665 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010570_Irs1 chr1 82229686 82300552 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010584_Itln1 chr1 173448254 173495879 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010600_Kcnh1 chr1 194014507 194368391 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010607_Kcnk2 chr1 191031813 191229415 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010629_Kifap3 chr1 165671988 165847216 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010633_Uhmk1 chr1 172123558 172145524 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010678_Aff3 chr1 38232856 38782360 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010683_Lamc1 chr1 155065803 155179906 - chr1 155123313 155123435 0 56471 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_010712_Lhx4 chr1 157520057 157598794 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010732_Lrrn2 chr1 134776870 134865321 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010766_Marco chr1 122261022 122466383 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010778_Cd46 chr1 196861976 196919007 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010827_Msc chr1 14520272 14746075 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010834_Mstn chr1 53118495 53124923 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010863_Myo1b chr1 51806622 51973696 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010865_Myoc chr1 164569268 164581467 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010879_Nck2 chr1 43501442 43627345 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010880_Ncl chr1 88241155 88255995 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010892_Nek2 chr1 193645343 193656921 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010916_Nhlh1 chr1 173982425 173987707 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010933_Nppc chr1 88512597 88567147 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011011_Oprk1 chr1 5578025 5596202 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011063_Pea15a chr1 174126043 174136915 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011066_Per2 chr1 93312559 93386413 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011070_Pfdn2 chr1 173275115 173289384 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011082_Pigr chr1 132723238 132748826 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011086_Pikfyve chr1 65225807 65332228 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011111_Serpinb2 chr1 109407675 109422169 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011198_Ptgs2 chr1 151947054 152026155 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011206_Ptpn18 chr1 34516613 34532568 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011267_Rgs16 chr1 155574693 155592596 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011273_Xpr1 chr1 157103002 157264554 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011277_Rnf2 chr1 153305192 153359013 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011283_Rp1 chr1 3989638 4469288 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011318_Apcs chr1 174824092 174855560 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011345_Sele chr1 165978323 165988607 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011346_Sell chr1 165992132 166007817 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011347_Selp chr1 166045416 166080154 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011439_Sox13 chr1 135278853 135384763 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011441_Sox17 chr1 4481009 4487839 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011459_Serpinb8 chr1 109486542 109586251 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011465_Spna1 chr1 176102906 176178561 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011487_Stat4 chr1 52036485 52164030 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011494_Stk16 chr1 75207414 75212181 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011541_Tcea1 chr1 4847584 4889703 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011590_Timm17a chr1 137197272 137210335 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011633_Traf5 chr1 193821096 193916369 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011650_Tsn chr1 120194658 120208016 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011729_Ercc5 chr1 44204270 44256568 + chr1 44195449 44195639 8631 8631 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_011770_Ikzf2 chr1 69574124 69733875 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011780_Adam23 chr1 63482194 63639230 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011780_Adam23 chr1 63640970 63642850 + chr1 63664888 63665018 22038 23918 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_011785_Akt3 chr1 178940936 179188314 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011794_Bpnt1 chr1 187156058 187181696 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011796_Capn10 chr1 94830953 94844518 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011800_Cdh20 chr1 106665116 106892058 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011804_Creg1 chr1 167693878 167710825 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011811_Farsb chr1 78414533 78506689 - chr1 78630893 78631160 124204 124204 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_011825_Grem2 chr1 176763926 176859770 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011880_Rgs7 chr1 176989221 177422985 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011882_Rnasel chr1 155596576 155619417 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011931_Rfwd2 chr1 161159948 161307408 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011935_Esrrg chr1 189432683 190062059 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_012009_Sh2d1b1 chr1 172162900 172220030 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_012012_Exo1 chr1 177810732 177841721 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_012049_Nit1 chr1 173270709 173276021 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_012058_Srp9 chr1 183988019 184062514 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013474_Apoa2 chr1 173151908 173156502 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013489_Cd84 chr1 173769848 173820852 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013499_Cr1l chr1 196924298 196957754 - chr1 197057796 197057843 100042 100042 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_013612_Slc11a1 chr1 74421758 74433050 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013626_Pam chr1 99691711 100053468 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013673_Sp100 chr1 84943347 87618694 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013715_Cops5 chr1 10014683 10028315 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013729_Mixl1 chr1 182623184 182634680 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013730_Slamf1 chr1 173682982 173731471 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013750_Phlda3 chr1 137662671 137665710 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013784_Pign chr1 107385512 107560244 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013835_Trove2 chr1 145597816 145624178 - chr1 145591041 145591176 6640 33002 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_013862_Rabgap1l chr1 162149308 162739582 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013919_Usp21 chr1 173212080 173218102 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_015750_Neu2 chr1 89348720 89494397 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_015780_Cfhr1 chr1 141443639 141456806 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_015811_Rgs1 chr1 146060709 146118313 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_015818_Hs6st1 chr1 36125255 36163289 + chr1 36106813 36107058 18197 18197 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_016696_Gpc1 chr1 94728253 94757346 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016702_Agxt chr1 95031777 95041991 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016716_Cul3 chr1 80261498 80323399 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016717_Scly chr1 93192544 93217635 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016749_Mybph chr1 136090025 136097809 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016778_Bok chr1 95579016 95592340 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016796_Vamp4 chr1 164500371 164532593 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016805_Hnrnpu chr1 180251245 180298730 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016846_Rgl1 chr1 154357421 154613475 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016851_Irf6 chr1 194979326 194998230 + chr1 194957396 194957723 21603 21603 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_016894_Ramp1 chr1 93076419 93120251 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016894_Ramp1 chr1 93120257 93121772 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016916_Blcap chr1 46068602 46087314 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016917_Slc40a1 chr1 45964925 45999090 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016923_Ly96 chr1 16678152 16699618 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016928_Tlr5 chr1 184884929 184903333 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016960_Ccl20 chr1 83112527 83138624 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_017480_Icos chr1 61034747 61057162 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018729_Cd244 chr1 173481630 173515439 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018750_Rassf5 chr1 133072991 133144761 - chr1 133114860 133115015 0 29746 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_018775_Tbc1d8 chr1 39428350 39544345 - chr1 39492140 39492513 0 51832 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_018796_Eef1b2 chr1 63221360 63227060 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018817_Smarcal1 chr1 72629842 72679806 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018868_Nop58 chr1 59741819 59769026 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018872_Tmem131 chr1 36841788 37000491 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018881_Fmo2 chr1 164804452 164828875 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019432_Tmem37 chr1 121962801 121979194 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019445_Fmn2 chr1 176431685 176752860 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019479_Hes6 chr1 93308097 93310595 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019484_Refbp2 chr1 173433397 173434881 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019562_Uchl5 chr1 145623774 145654586 + chr1 145591041 145591176 32598 32598 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_019570_Rev1 chr1 38109638 38186507 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019645_Pkp1 chr1 137767972 137815881 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019685_Ruvbl1 chr1 141824644 141826247 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019759_Dpt chr1 166726785 166754377 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019777_Ikbke chr1 133151052 133176163 - chr1 133114860 133115015 36037 61148 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_019790_Tmeff2 chr1 50957501 51282275 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019933_Ptpn4 chr1 121556050 121771541 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019993_Aldh9a1 chr1 169280142 169298663 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_020025_B3galt2 chr1 145487786 145497516 + chr1 145591041 145591176 93525 103255 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_020579_B4galt3 chr1 173199650 173207025 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_020588_Tmem183a chr1 136242675 136258707 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_020604_Jph1 chr1 16837549 17087942 - chr1 17030405 17030545 0 57397 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_021285_Myl1 chr1 66948125 66992032 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021295_Lancl1 chr1 67004053 67085447 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021306_Ecel1 chr1 89039384 89053076 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021312_Wdr12 chr1 60099363 60155552 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021313_Rnf25 chr1 74640329 74648026 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021342_Kcne4 chr1 78791793 78816579 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021350_Chml chr1 177615948 177618649 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021374_Rgs20 chr1 4899617 5060346 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021380_Il20 chr1 132803344 132808275 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021383_Rqcd1 chr1 74542393 74577404 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021400_Prg4 chr1 152296956 152333784 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021408_Ush2a chr1 190085902 190292167 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021421_Angel2 chr1 192748297 192770827 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021433_Stx6 chr1 157005819 157054716 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021467_Tnni1 chr1 137676021 137713725 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021511_Rrs1 chr1 9535513 9537532 + chr1 9619046 9619167 81514 83533 U NO chr1 9619175 9619382 81643 83662 U NO . . . . . . . . . . . . . .
+NM_021537_Stk25 chr1 95517348 95555233 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021541_Cryba2 chr1 74936508 74939802 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021600_Chrnd chr1 89087192 89096645 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021605_Nek7 chr1 140379472 140516775 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021607_Ncstn chr1 173996154 174012927 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021610_Gpa33 chr1 168060559 168118074 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022018_Fam129a chr1 153370940 153589282 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022019_Dusp10 chr1 185755009 185899515 + chr1 185854947 185855105 0 99938 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_022312_Tnr chr1 161327058 161857057 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022320_Gpr35 chr1 94683531 94882968 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022327_Ralb chr1 121363651 121401351 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022329_Ifrg15 chr1 157883344 157900866 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022417_Itm2c chr1 87780787 87838221 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022563_Ddr2 chr1 171907607 172040752 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022721_Fzd5 chr1 64777130 64826549 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022881_Rgs18 chr1 146599793 146755382 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022988_Nif3l1 chr1 58501750 58538650 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023041_Pex19 chr1 174056859 174067189 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023141_Tor3a chr1 158583760 158604477 - chr1 158580638 158580759 3001 23718 U NO chr1 158537267 158537411 46349 67066 U NO chr1 158510523 158510813 72947 93664 U NO . . . . . . .
+NM_023173_Dusp12 chr1 172803629 172815650 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023200_Ppp1r7 chr1 95239431 95266345 + chr1 95186508 95186637 52794 52794 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_023284_Nuf2 chr1 171386224 171461676 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023314_Eif4e2 chr1 89110486 89145136 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023341_Cabc1 chr1 182095369 182129713 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023343_Ilkap chr1 93270445 93290447 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023434_Tox4 chr1 16757104 16760219 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023514_Mrps9 chr1 42760822 42962528 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023523_Pecr chr1 72281105 72330878 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023617_Aox3 chr1 58169980 58259027 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023631_Aox4 chr1 58267261 58325441 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023645_Kdelc1 chr1 44143458 44177102 - chr1 44195449 44195639 18347 18347 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_023727_Rd3 chr1 193784705 193812153 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023732_Abcb6 chr1 75168223 75177000 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023755_Tcfcp2l1 chr1 120524515 120655075 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023884_Ralgps2 chr1 158734300 158969600 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_024197_Ndufa10 chr1 94121208 94393553 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_024264_Cyp27a1 chr1 74759770 74786412 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_024282_Pppde1 chr1 180117558 180197483 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_024283_1500015O10Rik chr1 43787414 43799399 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025283_Mobkl3 chr1 55187734 55211736 + chr1 55283572 55283675 71836 95838 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_025300_Mrpl15 chr1 4763290 4798011 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025303_Stau2 chr1 16218775 16510193 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025321_Sdhc chr1 173057297 173080736 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025386_Fbxo36 chr1 84835492 84897059 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025388_Ufc1 chr1 173218698 173225135 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025424_Nenf chr1 193130454 193141997 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025439_Tmem9 chr1 137879942 137931919 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025453_Tm4sf20 chr1 82749860 82765031 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025454_Ing5 chr1 95700534 95719794 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025470_1810030J14Rik chr1 176260650 176349219 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025474_Mrps14 chr1 162082365 162131317 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025505_Blzf1 chr1 166219931 166237615 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025557_Pcp4l1 chr1 173103394 173126370 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025569_Mgst3 chr1 169302037 169323952 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025596_Prelid1 chr1 63410974 63469460 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025597_Ndufb3 chr1 58631453 58653239 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025677_Tsen15 chr1 154217920 154233812 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025683_Rpe chr1 66747223 66839854 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025746_4933415F23Rik chr1 23107346 23263222 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025773_Ube2w chr1 16530881 16609419 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025784_Bcs1l chr1 74634010 74639375 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025819_1200016B10Rik chr1 153214763 153304502 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025864_Tmem206 chr1 193149566 193176819 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025867_Serpinb11 chr1 109246610 109277052 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025920_Thap4 chr1 95602021 95651542 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025964_Fam119a chr1 64653048 64670990 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026024_Ube2t chr1 136857731 136870739 + chr1 136956468 136956598 85729 98737 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_026041_Rrp15 chr1 188544857 188573732 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026078_Pigc chr1 163860747 163957217 + chr1 163827897 163828062 32685 32685 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_026123_Unc50 chr1 37486671 37504876 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026171_Nvl chr1 183008557 183074318 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026187_Ankzf1 chr1 75188977 75192143 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026187_Ankzf1 chr1 75192524 75195962 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026195_Atic chr1 71584010 71626205 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026234_Pigm chr1 174306609 174314210 + chr1 174376470 174376659 62260 69861 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_026241_Ankrd39 chr1 36594353 36604077 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026250_Zh2c2 chr1 99658035 99706130 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026321_Fam174a chr1 97174825 97346168 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026367_Gpatch2 chr1 189010707 189180483 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026369_Arpc5 chr1 154613024 154638792 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026375_Ahctf1 chr1 181675025 181733948 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026380_Rgs8 chr1 155468581 155563679 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026390_Ubxn4 chr1 130140557 130175951 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026430_Uxs1 chr1 43804890 43884625 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026454_Ube2f chr1 93146888 93187187 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026456_Tceb1 chr1 16603307 16655630 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026472_Mki67ip chr1 120218436 120230401 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026493_Cspp1 chr1 10028093 10126849 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026500_Ddx59 chr1 138242798 138336799 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026503_1110058L19Rik chr1 24002785 24017210 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026626_Efcab2 chr1 180335927 180414624 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026680_Golt1a chr1 135206322 135226478 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026713_Mogat1 chr1 78496730 78564215 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026719_Lmbrd1 chr1 24593456 24847969 + chr1 24609562 24609623 0 16106 . YES chr1 24609923 24609992 0 16467 . YES . . . . . . . . . . . . . .
+NM_026719_Lmbrd1 chr1 24820582 24823143 + chr1 24730996 24731077 89505 89505 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_026725_Dusp23 chr1 174560902 174563119 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026796_Smyd2 chr1 191704373 191746222 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026823_Arl8a chr1 137043216 137053347 + chr1 136956468 136956598 86618 86618 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_026846_Zfand2b chr1 75165237 75168196 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026850_Pdcl3 chr1 39044622 39054081 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026913_Mitd1 chr1 37931656 37947242 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026977_1810031K17Rik chr1 75131500 75139270 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027098_Mrpl30 chr1 37947313 37959167 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027154_Tmbim1 chr1 74334823 74352176 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027159_Ccdc115 chr1 34491854 34496517 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027188_Smyd3 chr1 180885172 181448168 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027300_Spata3 chr1 87913403 87926533 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027351_Ppil3 chr1 58486110 58502330 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027357_Psmd1 chr1 87958636 88174849 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027407_Ica1l chr1 60039354 60099956 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027415_Tmem70 chr1 16610621 16668358 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027430_Brp44 chr1 167390752 167411345 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027534_Kdsr chr1 108617007 108656357 - chr1 108747519 108747791 91162 91162 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_027548_Serpinb7 chr1 109296172 109349266 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027551_Klhl30 chr1 93244259 93259068 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027637_4931428L18Rik chr1 31197921 31279501 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027661_Hsfy2 chr1 56668158 56822175 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027677_Gpr39 chr1 127573518 127795359 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027678_Zranb3 chr1 129846941 130025531 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027725_Wdr69 chr1 83156310 83207145 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027884_Tns1 chr1 73956820 74144891 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027886_Stk11ip chr1 75518100 75533910 + chr1 75481920 75482054 36046 36046 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_027893_Pvrl4 chr1 173292993 173318729 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027921_Slc16a14 chr1 84902046 84931841 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027971_Serpinb12 chr1 108831026 108853655 + chr1 108747519 108747791 83235 83235 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_027979_Chit1 chr1 136007829 136048117 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028057_Cyb5r1 chr1 136302358 136308302 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028091_Osgepl1 chr1 53370488 53383184 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028135_Tmem163 chr1 129382910 129574703 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028173_Tram1 chr1 13554779 13579965 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028250_Acbd6 chr1 157358146 157536633 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028320_Adipor1 chr1 136311830 136329944 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028333_Angptl1 chr1 158769061 158791209 + chr1 158835251 158835391 44042 66190 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_028399_Ccnt2 chr1 129670253 129704638 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028408_Cnih3 chr1 183282759 183419790 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028450_Gulp1 chr1 44608366 44896390 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028534_Smap1 chr1 23833022 23929292 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028696_Obfc2a chr1 51417024 51550602 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028713_Rftn2 chr1 55227030 55283748 - chr1 55283572 55283675 0 73 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_028717_Als2 chr1 59219131 59294111 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028749_Npl chr1 155350145 155424001 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028776_Scyl3 chr1 165859251 165885242 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028776_Scyl3 chr1 165876143 165924907 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028778_Nuak2 chr1 134212715 134241254 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028787_Slc35f5 chr1 127332249 127554856 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028817_Acsl3 chr1 78654388 78743434 + chr1 78630893 78631160 23228 23228 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_028829_Paqr8 chr1 20811519 20929711 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028848_Spata17 chr1 188868366 189039831 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028889_Efhd1 chr1 89160561 89207413 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028942_Slco6c1 chr1 98899133 99024880 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029025_Tmem81 chr1 134402623 134405216 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029084_Slamf8 chr1 174510275 174520700 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029115_4930455F23Rik chr1 166205721 166217973 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029160_Spag16 chr1 69873526 70771706 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029269_Spp2 chr1 90303568 90373213 + chr1 90412932 90413132 39719 109364 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_029398_Tmem14a chr1 21143538 21220248 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029409_Mff chr1 82721393 82748958 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029612_Slamf9 chr1 174392516 174408706 + chr1 174376470 174376659 15857 15857 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_029696_Mdh1b chr1 63745401 63776894 - chr1 63664888 63665018 80383 111876 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_029756_Sdccag8 chr1 178743478 178953256 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029766_Dtl chr1 193272523 193399423 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029846_Atg16l1 chr1 89652465 89697344 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029888_Zfp142 chr1 74612492 74634794 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030013_Cyp20a1 chr1 60400175 60444904 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030025_Ccdc150 chr1 54251865 54451794 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030060_Batf3 chr1 192921746 192944913 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030131_Cnih4 chr1 183074401 183099213 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030211_Kctd18 chr1 58007830 58075790 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030245_Tada1l chr1 168309248 168323752 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030266_Inpp4a chr1 37356703 37476203 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030556_Slc19a3 chr1 83001155 83083196 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030676_Nr5a2 chr1 138739149 138950879 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030710_Slamf6 chr1 173847613 173932462 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030724_Uck2 chr1 169106790 169215431 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_031164_F13b chr1 141398326 141420329 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_031179_Sf3b1 chr1 55042016 55084369 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_031189_Myog chr1 136186558 136189125 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_031192_Ren1 chr1 135246578 135256895 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_031402_Crispld1 chr1 17717123 17756425 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_032005_Tbx19 chr1 167056323 167090894 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_033077_D1Pas1 chr1 188791295 188934742 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_033509_Vangl2 chr1 173931096 173977129 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_033563_Klf7 chr1 64049920 64169179 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_033570_Cnnm4 chr1 36528452 36565609 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_033608_Igsf9 chr1 174411686 174429005 + chr1 174376470 174376659 35027 35027 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_033652_Lmx1a chr1 169579767 169778872 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053015_Mlph chr1 92811657 92847814 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053095_Il24 chr1 132778072 132784021 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053106_Lmod1 chr1 137221395 137264642 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053107_Gpr45 chr1 43009719 43092301 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053191_Pi15 chr1 17591992 17621000 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053199_Cadm3 chr1 175264723 175362523 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053257_Rpl31 chr1 39421000 39429094 + chr1 39492140 39492513 63046 71140 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_053270_Rims1 chr1 22275987 22813178 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_054076_Optc chr1 135787973 135805299 - chr1 135851853 135852218 46554 46554 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_054077_Prelp chr1 135806855 135865173 - chr1 135851853 135852218 0 12955 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_054087_Slc19a2 chr1 166178694 166196022 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_054102_Ivns1abp chr1 153196503 153212127 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_080419_Igsf8 chr1 174191772 174249967 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_080844_Serpinc1 chr1 162908738 162946004 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_080850_Pask chr1 95205357 95240039 - chr1 95186508 95186637 18720 53402 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_130456_Nphs2 chr1 158233397 158258162 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_130890_Capn8 chr1 184489366 184629001 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133193_Il1rl2 chr1 40381454 40447345 + chr1 40325917 40326123 55331 55331 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_133220_Sgk3 chr1 9787936 9890911 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133225_Acbd3 chr1 182654006 182684317 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133235_Khdrbs2 chr1 32113056 32771277 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133239_Crb1 chr1 141093643 141296750 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133252_Tram2 chr1 20984161 21069306 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133358_Zfp617 chr1 87909957 87912999 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133664_Lad1 chr1 137715163 137730085 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133684_Mosc2 chr1 186636947 186687141 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133705_Pycr2 chr1 182834431 182850616 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133728_Asnsd1 chr1 53382361 53409576 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133748_Insig2 chr1 123200933 123229157 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133780_Tpr chr1 152239968 152298193 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133781_Cab39 chr1 87687678 87748148 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133805_Cops8 chr1 92499556 92564446 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133806_Uap1 chr1 172007106 172105098 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133808_Hdlbp chr1 95302520 95375513 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133809_Kmo chr1 177550532 177592237 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133810_Stk17b chr1 53812356 53857070 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133815_Lbr chr1 183737722 183773157 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133816_Sh3bp4 chr1 90966984 91051778 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133817_Zfp451 chr1 33817052 33871530 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133819_Ppp1r15b chr1 135027595 135036355 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133826_Atp6v1h chr1 5060109 5173662 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133828_Creb1 chr1 64579391 64645546 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133828_Creb1 chr1 64646684 64649524 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133829_Mfsd6 chr1 52702101 52784383 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133832_Rdh10 chr1 16095419 16123815 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133975_Trip12 chr1 84717781 84836834 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_134252_Trpm8 chr1 90181363 90285482 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_134438_Gpr37l1 chr1 137054243 137069087 - chr1 136956468 136956598 97645 112489 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_134448_Dst chr1 33965107 34411632 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_138314_Nme7 chr1 166237503 166369483 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_138741_Sdpr chr1 51345970 51359791 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_139146_Satb2 chr1 56850830 57044309 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_139150_Carf chr1 60155057 60208366 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_139152_Asb18 chr1 91849253 91911152 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_139270_Pth2r chr1 65328648 65436194 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144530_Zc3h11a chr1 135516445 135557956 - chr1 135582677 135582828 24721 24721 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_144539_Slamf7 chr1 173562534 173583396 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144558_Bivm chr1 44175822 44201615 + chr1 44195449 44195639 0 19627 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_144559_Fcgr4 chr1 172925278 172974678 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144761_Crygb chr1 65126809 65127141 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144791_Tor1aip1 chr1 157851734 157889804 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144794_Tmem63a chr1 182872430 182919700 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144796_Susd4 chr1 184694011 184850523 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144810_Klhdc8a chr1 134182914 134204342 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144814_Rcor3 chr1 193910981 193962565 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144817_Camk1g chr1 195172540 195216632 - chr1 195324443 195324741 107811 107811 D NO chr1 195330701 195330930 114069 114069 D NO chr1 195338316 195338616 121684 121684 D NO chr1 195342728 195342985 126096 126096 D NO
+NM_144875_Rab7l1 chr1 133763813 133782396 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144877_Mettl13 chr1 164462268 164478659 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144878_Fmo4 chr1 164675648 164744002 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144879_Vash2 chr1 192771545 192803413 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144880_Ppp2r5a chr1 193175865 193290728 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144881_Hhat chr1 194320603 194649833 - chr1 194645118 194645475 0 4358 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_144882_2810022L02Rik chr1 57831026 58005952 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144953_1700019D03Rik chr1 52981207 53077002 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144960_Fcamr chr1 132697479 132711317 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145100_Lypd1 chr1 127768620 127809650 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145128_Mgat5 chr1 129101583 129384133 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145141_Fcrla chr1 172847725 172857714 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145142_Chst10 chr1 38920721 38955057 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145143_Mpp4 chr1 59177791 59218762 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145222_B3gnt7 chr1 88199427 88203870 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145381_Lactb2 chr1 13604244 13650616 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145392_Bag2 chr1 33802345 33814648 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145413_Fam20b chr1 158608676 158649180 - chr1 158580638 158580759 27917 68421 U NO chr1 158537267 158537411 71265 111769 U NO . . . . . . . . . . . . . .
+NM_145415_AA408296 chr1 194918802 194956446 - chr1 194957396 194957723 950 950 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_145417_Rnpep chr1 137159304 137180985 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145506_Epb4.1l5 chr1 121437741 121545557 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145508_Dyrk3 chr1 133018921 133034897 - chr1 133114860 133115015 79963 79963 D NO chr1 132950929 132951247 67674 83650 U NO . . . . . . . . . . . . . .
+NM_145509_5430435G22Rik chr1 133585272 133610099 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145510_Rabif chr1 136391105 136405512 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145511_BC003331 chr1 152183263 152240229 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145512_Sft2d2 chr1 167104119 167124549 - chr1 167222964 167223261 98415 98415 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_145513_Tiprl chr1 167133855 167183116 - chr1 167222964 167223261 39848 39848 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_145514_Wdr26 chr1 183100306 183150525 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145515_Mark1 chr1 186720345 186823408 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145516_Plekhb2 chr1 34906787 34936422 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145517_Ormdl1 chr1 53353438 53367153 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145518_Ndufs1 chr1 63190187 63223454 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145519_Farp2 chr1 95408676 95518914 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145624_Zfp709 chr1 87911157 87911749 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145692_Lrrc67 chr1 9943781 9999420 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145856_Il17f chr1 20767237 20776566 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145977_Slc45a3 chr1 133859512 133879541 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145991_Cdc73 chr1 145274292 145549936 - chr1 145591041 145591176 41105 41105 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_145996_Arid5a chr1 36359349 36380874 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146103_Tmem185b chr1 121396063 121425550 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146106_Lyplal1 chr1 187911630 187941208 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146107_Actr1b chr1 36754975 36766847 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146108_Hibch chr1 52899113 52977830 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146110_Aamp chr1 74326421 74331613 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146112_Gigyf2 chr1 89223593 89347370 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146250_Gpr1 chr1 63229165 63309823 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146277_Olfr1412 chr1 94484843 94486082 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146305_Olfr420 chr1 176088784 176089871 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146490_Olfr1411 chr1 94493008 94494065 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146491_Olfr1410 chr1 94504416 94505384 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146715_Olfr419 chr1 176180115 176200418 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146716_Olfr432 chr1 175977437 175981444 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146717_Olfr433 chr1 175971174 175973629 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146718_Olfr430 chr1 175999350 176000384 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146720_Olfr421 chr1 176072364 176082596 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146721_Olfr424 chr1 176057388 176067824 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146722_Olfr429 chr1 176019173 176020111 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146761_Olfr414 chr1 176360513 176361670 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146764_Olfr1408 chr1 175060414 175083388 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146881_Olfr1404 chr1 175145784 175146725 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_147037_Olfr1413 chr1 94469750 94470721 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_148937_Plcd4 chr1 74589462 74614368 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_152895_Kdm5b chr1 136455975 136529487 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_152915_Dner chr1 84366415 84706993 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153064_Ndufs2 chr1 173164989 173180188 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153088_Ctdsp1 chr1 74438065 74443852 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153111_Fev chr1 74915158 74932371 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153114_Otos chr1 94540797 94553072 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153137_Traf3ip3 chr1 195001656 195027877 - chr1 194957396 194957723 43933 70154 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_153154_Tcfap2d chr1 19027377 19157044 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153171_Rgs13 chr1 145985803 146024550 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153179_Pkhd1 chr1 20040166 20661582 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153408_Neurl3 chr1 36321504 36355139 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153502_Ankrd23 chr1 36587038 36593708 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153530_Dis3l2 chr1 88570607 88946671 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153539_Fam5c chr1 148341910 148749599 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153555_Wdr42a chr1 174078166 174127554 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153556_Pms1 chr1 53245508 53353841 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153601_Lgsn chr1 31221394 31261688 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153744_Prkag3 chr1 74785516 74825109 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153774_Ipo9 chr1 137278207 137330146 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_170597_Creg2 chr1 39677083 39708307 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_170755_Fam134a chr1 75137484 75144869 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172054_Txndc9 chr1 38041434 38054101 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172124_B3gat2 chr1 23755411 23855977 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172294_Sulf1 chr1 12708560 12851249 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172406_Trak2 chr1 58955979 59031177 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172422_Fastkd2 chr1 63777134 63803028 + chr1 63664888 63665018 112116 112116 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_172430_Sphkap chr1 83207585 83404745 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172463_Sned1 chr1 95132418 95197642 + chr1 95186508 95186637 0 54090 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_172484_E030049G20Rik chr1 127810213 128389504 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172485_Thsd7b chr1 131169889 132172070 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172499_Mfsd9 chr1 40828883 40921070 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172510_Mfsd4 chr1 133919383 133964629 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172513_Fam126b chr1 58575029 58643157 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172516_Dstyk chr1 134314046 134363525 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172517_Rbbp5 chr1 134368568 134402423 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172643_Zbtb41 chr1 141318960 141349577 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172644_Dars2 chr1 162970732 163001279 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172647_F11r chr1 173365700 173394971 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172648_Ifi205 chr1 175664572 175958593 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172650_Kctd3 chr1 190794974 190831710 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172652_4632411B12Rik chr1 36381585 36426026 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172653_Slc39a10 chr1 46863572 46949677 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172656_Stradb chr1 59012025 59052817 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172841_Slco5a1 chr1 12857471 12982812 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172843_Tor1aip2 chr1 157906541 157915942 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172844_Fmo9 chr1 168589849 168611976 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172845_Adamts4 chr1 173178880 173192383 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172846_Dnahc14 chr1 183669052 183694102 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172850_Ankmy1 chr1 94757771 94799473 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172851_Cntnap5b chr1 101934704 102382815 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172852_Serpinb13 chr1 108877561 108897772 + chr1 108747519 108747791 129770 129770 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_172853_Cdh7 chr1 111718165 112036714 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172974_Cops7b chr1 88478926 88503950 + chr1 88408969 88409267 69659 69659 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_173029_Adcy10 chr1 167415324 167506904 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173187_2310035C23Rik chr1 107560448 107651751 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173378_Trp53bp2 chr1 184333536 184392728 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173395_Fam132b chr1 93263007 93270794 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173424_Zbtb37 chr1 162938038 162965197 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173425_Fam124b chr1 80156958 80214611 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173437_Nav1 chr1 137332309 137482282 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173437_Nav1 chr1 137481360 137496527 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173443_Vcpip1 chr1 9709587 9764569 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173760_Hisppd1 chr1 99592475 99667685 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173771_4933406M09Rik chr1 136282517 136287560 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173772_Neu4 chr1 95917070 95928707 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173865_Slc41a1 chr1 133724090 133745438 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173868_St18 chr1 6477297 6885001 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173870_Mgat4a chr1 37496234 37609425 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_174874_Atg4b chr1 95648097 95687167 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_174985_Gpbar1 chr1 74321873 74326272 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175031_Stk36 chr1 74648039 74683468 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175106_Tmem177 chr1 121793019 121809709 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175118_Dusp28 chr1 94803563 94805012 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175127_Fbxo28 chr1 184242976 184303818 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175170_Pogk chr1 168314763 168391350 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175200_Als2cr11 chr1 59053967 59151744 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175210_Abca12 chr1 71207671 71501632 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175236_Adhfe1 chr1 9538049 9570746 + chr1 9619046 9619167 48300 80997 U NO chr1 9619175 9619382 48429 81126 U NO . . . . . . . . . . . . . .
+NM_175259_Shisa4 chr1 137267654 137274885 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175293_D630023F18Rik chr1 65151863 65176420 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175294_Nucks1 chr1 133807079 133832888 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175296_Mael chr1 168115771 168178081 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175370_Als2cr12 chr1 58714975 58752801 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175382_2700049P18Rik chr1 133344141 133436449 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175439_Mars2 chr1 55294084 55297625 + chr1 55283572 55283675 10409 10409 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_175443_Etnk2 chr1 135260167 135276893 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175460_Nmnat2 chr1 154802128 154966391 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175461_Fam78b chr1 168898096 169021408 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175564_Tmem169 chr1 72330953 72349677 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175642_Bai3 chr1 25084207 25887514 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175686_Prrx1 chr1 165175252 165245859 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_176916_Pld5 chr1 177892457 178205403 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_176972_Usp37 chr1 74482084 74590860 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_176980_Ankar chr1 72689581 72747143 - chr1 72769824 72770056 22681 22681 D NO chr1 72770058 72770226 22915 22915 D NO chr1 72815517 72815742 68374 68374 D NO . . . . . . .
+NM_177068_Olfml2b chr1 172569075 172612915 + chr1 172620779 172620912 7864 51704 U NO chr1 172620917 172621080 8002 51842 U NO . . . . . . . . . . . . . .
+NM_177084_Slc9a4 chr1 40636956 40687551 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177129_Cntn2 chr1 134406005 134442705 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177164_A830006F12Rik chr1 70772309 70929065 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177173_A830018L16Rik chr1 11404178 11994163 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177235_Bend6 chr1 33903283 33964764 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177243_Slc26a9 chr1 133640599 133668075 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177305_Arl4c chr1 90569702 90617572 - chr1 90592499 90592629 0 24943 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_177397_Atp6v1g3 chr1 140120875 140186039 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177445_Dars chr1 130260284 130314013 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177587_Aqp12 chr1 94886487 94908846 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177604_AA986860 chr1 132628563 132644539 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177643_Zfp281 chr1 138487073 138526617 + chr1 138437726 138437860 49213 49213 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_177646_Dgkd chr1 89749836 89841946 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177722_6030422M02Rik chr1 9898713 9932156 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177723_Vsig8 chr1 174486069 174513273 + chr1 174376470 174376659 109410 109410 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_177724_D230039L06Rik chr1 180426979 180686112 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177756_Glt25d2 chr1 154223175 154357825 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177757_Kif26b chr1 180720593 180862983 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177781_Trpa1 chr1 14861962 14909072 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177834_Cpa6 chr1 10314801 10710026 - chr1 10617233 10617437 0 92589 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_177838_Fam163a chr1 157923096 158135544 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177839_Tnn chr1 161966935 162084477 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178051_Mterfd2 chr1 95195779 95202630 - chr1 95186508 95186637 9142 15993 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_178055_Dnajb2 chr1 75233016 75242264 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178119_Agap1 chr1 91351421 91791845 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178241_Il8ra chr1 74238380 74241205 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178243_5830403L16Rik chr1 155697272 155747352 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178244_Teddm1 chr1 155724147 155740188 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178399_3110035E14Rik chr1 9591248 9617222 + chr1 9619046 9619167 1824 27798 U NO chr1 9619175 9619382 1953 27927 U NO . . . . . . . . . . . . . .
+NM_178405_Atp1a2 chr1 174201852 174233438 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178593_Rcsd1 chr1 167572007 167639868 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178598_Tagln2 chr1 174430123 174475991 + chr1 174376470 174376659 53464 53464 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_178601_Imp4 chr1 34496377 34511555 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178632_Ints7 chr1 193399085 193447550 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178653_Sccpdh chr1 181598088 181617593 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178690_Rab3gap1 chr1 129765355 129840723 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178691_Yod1 chr1 132612680 132618643 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178692_C130074G19Rik chr1 186695805 186707077 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178775_Rps6kc1 chr1 192524091 192736016 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178779_Rnf152 chr1 107176426 107253513 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178874_Tmcc2 chr1 134252895 134288369 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178883_Gorab chr1 165315039 165340946 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178884_Obsl1 chr1 75482401 75503218 - chr1 75481920 75482054 347 21164 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_181405_Rnpepl1 chr1 94807467 94817954 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_181546_Syt14 chr1 194713536 194861959 - chr1 194957396 194957723 95437 95437 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_181750_R3hdm1 chr1 129999892 130134312 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_181796_Gstp2 chr1 193897651 193905509 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_182716_Nfasc chr1 134445291 134638354 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_182930_Plekha6 chr1 135077806 135200008 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183019_Arhgef4 chr1 34788954 34873560 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183022_Accn4 chr1 75447063 75470207 + chr1 75481920 75482054 11713 34857 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_183027_Ap1s3 chr1 79591820 79668545 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183028_Pcmtd1 chr1 7079053 7163709 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183124_Defb41 chr1 18241071 18350659 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183355_Pbx1 chr1 170049495 170512777 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183391_Tnfsf18 chr1 163373523 163524094 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_194333_Slc23a3 chr1 75120731 75130464 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198006_6330578E17Rik chr1 37473934 37474944 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198006_6330578E17Rik chr1 37477057 37486928 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198028_Serpinb10 chr1 109425580 109445838 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198127_Abi2 chr1 60466022 60537998 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198247_Sertad4 chr1 194670313 194693726 - chr1 194645118 194645475 24838 48251 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_198303_Eif5b chr1 38054627 38112414 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198652_6430706D22Rik chr1 90158880 90174174 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198653_Iars2 chr1 187109458 187153280 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198654_Nsl1 chr1 192886918 192919389 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198680_Serpinb3b chr1 109033488 109059720 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198899_Ugcgl1 chr1 36196873 36301555 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198934_Pou2f1 chr1 167804181 167932753 - chr1 167906284 167906554 0 26199 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_199007_Sgol2 chr1 58026657 58085164 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_199021_Dpp10 chr1 125044486 126749525 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_201363_Serpinb3c chr1 109088051 109198931 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_201376_Serpinb3d chr1 108974770 108980057 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_201641_Ugt1a10 chr1 89922380 90115570 + chr1 89989553 89989714 0 67173 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_206896_Olfr12 chr1 94516341 94538591 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207031_Ano7 chr1 95270385 95302271 + chr1 95186508 95186637 83748 83748 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_207137_Olfr417 chr1 176299050 176299979 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207137_Olfr417 chr1 176321202 176322113 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207158_Olfr427 chr1 176028781 176030538 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207225_Hdac4 chr1 93755950 94103099 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207228_Tsga10 chr1 37783457 37922148 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207233_C1ql2 chr1 122196386 122239751 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207281_4832428D23Rik chr1 44260915 44515719 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207583_Fam5b chr1 160175402 160286644 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207653_Cflar chr1 58768296 58813658 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207653_Cflar chr1 58813703 58815725 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_213616_Atp2b4 chr1 135602265 135697538 - chr1 135582677 135582828 19437 114710 U NO . . . . . . . . . . . . . . . . . . . . .
+NR_002840_Gas5 chr1 162964758 162968663 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NR_002858_EG241041 chr1 21268965 21306401 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NR_002870_Dnm3os chr1 164119785 164155671 + chr1 164215623 164215935 59952 95838 U NO . . . . . . . . . . . . . . . . . . . . .
+NR_003623_EG277333 chr1 182251970 182262902 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NR_026896_4931440L10Rik chr1 136437533 136449760 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
diff -r 000000000000 -r 0abe6bac47a6 test-data/peaks_per_feature2.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peaks_per_feature2.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,980 @@
+#gene.id gene.chr gene.start gene.end gene.strand chr start end dist_closest dist_TSS direction in_the_gene
+AF064749_Col6a3 chr1 92566771 92800755 - --- --- --- --- --- --- ---
+AK015559_4930472D16Rik chr1 25020851 25021989 - --- --- --- --- --- --- ---
+AK030377_A330023F24Rik chr1 196781953 196826186 - --- --- --- --- --- --- ---
+AK080193_A530079E22Rik chr1 89401837 89403491 - --- --- --- --- --- --- ---
+AK082264_C230030N03Rik chr1 34735043 34781084 + --- --- --- --- --- --- ---
+BC006931_AI597479 chr1 43153807 43172843 + --- --- --- --- --- --- ---
+BC021773_Glb1l chr1 75193364 75207353 - --- --- --- --- --- --- ---
+BC023951_D1Ertd622e chr1 99540054 99558631 - --- --- --- --- --- --- ---
+BC028767_3110009E18Rik chr1 122017764 122114603 + --- --- --- --- --- --- ---
+BC031781_BC031781 chr1 182781250 182798240 + --- --- --- --- --- --- ---
+BC034187_BC035947 chr1 78493611 78497758 - --- --- --- --- --- --- ---
+BC043098_Fam168b chr1 34870072 34917183 - --- --- --- --- --- --- ---
+BC049091_D1Bwg0212e chr1 39592545 39603734 + chr1 39492140 39492513 100032 100032 D NO
+BC049713_Ankrd45 chr1 163072817 163099826 + --- --- --- --- --- --- ---
+BC050813_4921511C04Rik chr1 37157481 37244861 + --- --- --- --- --- --- ---
+BC051128_4921521F21Rik chr1 65059273 65079312 - --- --- --- --- --- --- ---
+BC052693_2810422O20Rik chr1 165924541 165927371 + --- --- --- --- --- --- ---
+BC052931_A630001G21Rik chr1 87601462 87674840 - --- --- --- --- --- --- ---
+BC053100_5730559C18Rik chr1 138110108 138130841 - --- --- --- --- --- --- ---
+BC054802_9630058J23Rik chr1 181476521 181558044 + --- --- --- --- --- --- ---
+BC055845_2810025M15Rik chr1 159342483 159350353 + chr1 159240736 159240866 101617 101617 D NO
+BC055955_A130010J15Rik chr1 194999663 195004015 + chr1 194957396 194957723 41940 41940 D NO
+BC057872_Rab3gap2 chr1 187028006 187110623 + --- --- --- --- --- --- ---
+BC058417_2610017I09Rik chr1 42648822 42751667 - --- --- --- --- --- --- ---
+BC059254_Phlpp chr1 108042052 108306367 + --- --- --- --- --- --- ---
+BC070435_Fam123c chr1 34620070 34671545 + --- --- --- --- --- --- ---
+BC070446_Fam135a chr1 24017617 24107170 - --- --- --- --- --- --- ---
+BC071241_9430016H08Rik chr1 57463192 57497936 + --- --- --- --- --- --- ---
+BC072639_2010300C02Rik chr1 37646877 37776659 - --- --- --- --- --- --- ---
+BC080290_5033414K04Rik chr1 84032539 84360735 - --- --- --- --- --- --- ---
+BC082310_9430031J16Rik chr1 81073525 81338329 + --- --- --- --- --- --- ---
+BC089525_2310007B03Rik chr1 95047933 95063386 - chr1 95186508 95186637 123122 123122 D NO
+BC089561_Cep350 chr1 157692096 157820375 - --- --- --- --- --- --- ---
+BC147491_A230074B11Rik chr1 37083441 37133840 + --- --- --- --- --- --- ---
+BC147657_9630028B13Rik chr1 187253234 187265698 - --- --- --- --- --- --- ---
+ENSMUST00000027997_Rgs5 chr1 171625108 171625913 + --- --- --- --- --- --- ---
+ENSMUST00000051203_1700001G17Rik chr1 33726669 33727551 + --- --- --- --- --- --- ---
+ENSMUST00000054333_A130050O07Rik chr1 139823828 139826840 + --- --- --- --- --- --- ---
+ENSMUST00000056879_C230029F24Rik chr1 49301475 49397265 + --- --- --- --- --- --- ---
+ENSMUST00000057543_A730013G03Rik chr1 194659323 194661397 - chr1 194645118 194645475 13848 15922 U NO
+ENSMUST00000062637_4930470H14Rik chr1 175156866 175201240 + --- --- --- --- --- --- ---
+ENSMUST00000070048_ENSMUSG00000056128 chr1 92571736 92576368 + --- --- --- --- --- --- ---
+ENSMUST00000070987_EG433384 chr1 183781705 183783320 - --- --- --- --- --- --- ---
+ENSMUST00000072395_Olfr1406 chr1 175113651 175120746 - --- --- --- --- --- --- ---
+ENSMUST00000094288_Wdr64 chr1 177654798 177798070 + --- --- --- --- --- --- ---
+ENSMUST00000094950_Pgap1 chr1 54529849 54614539 - chr1 54631692 54631815 17153 17153 D NO
+ENSMUST00000097776_Cnnm3 chr1 36567938 36585164 + --- --- --- --- --- --- ---
+EU429481_Igfn1 chr1 137825893 137890307 - --- --- --- --- --- --- ---
+FJ024495_Ildr2 chr1 168236882 168239692 - --- --- --- --- --- --- ---
+FJ210934_Unc80 chr1 66514856 66556109 + --- --- --- --- --- --- ---
+NM_001001565_Chpf chr1 75470923 75476437 - chr1 75481920 75482054 5483 5483 D NO
+NM_001001809_Olfr218 chr1 175130421 175134469 + --- --- --- --- --- --- ---
+NM_001001883_Hecw2 chr1 53867026 54252002 - --- --- --- --- --- --- ---
+NM_001003917_Atg9a chr1 75177439 75189181 - --- --- --- --- --- --- ---
+NM_001004173_Sgpp2 chr1 78306692 78416864 + --- --- --- --- --- --- ---
+NM_001005423_Mreg chr1 72170192 72258895 - --- --- --- --- --- --- ---
+NM_001005507_Smg7 chr1 154684125 154750410 - --- --- --- --- --- --- ---
+NM_001005508_Arhgap30 chr1 173319072 173340822 + --- --- --- --- --- --- ---
+NM_001005520_Olfr244 chr1 176032571 176067605 - --- --- --- --- --- --- ---
+NM_001008419_Aox3l1 chr1 58335180 58437083 + --- --- --- --- --- --- ---
+NM_001008426_EG433365 chr1 155721475 155724001 + --- --- --- --- --- --- ---
+NM_001008533_Adora1 chr1 136095799 136181661 - --- --- --- --- --- --- ---
+NM_001009940_Il19 chr1 132786042 132915234 - chr1 132950929 132951247 35695 35695 D NO
+NM_001011525_Olfr1415 chr1 94376258 94381054 - --- --- --- --- --- --- ---
+NM_001011525_Olfr1415 chr1 94407669 94418761 - --- --- --- --- --- --- ---
+NM_001011684_Nms chr1 38995917 39007113 + --- --- --- --- --- --- ---
+NM_001011873_Xkr9 chr1 13658862 13691794 + --- --- --- --- --- --- ---
+NM_001011874_Xkr4 chr1 3203722 3713108 - --- --- --- --- --- --- ---
+NM_001012330_Zfp238 chr1 179359958 179380892 + --- --- --- --- --- --- ---
+NM_001013374_Lman2l chr1 36362897 36502078 - --- --- --- --- --- --- ---
+NM_001013382_Lrrc52 chr1 169375806 169397136 - --- --- --- --- --- --- ---
+NM_001013771_Gm973 chr1 59573136 59693241 + --- --- --- --- --- --- ---
+NM_001013779_Aim2 chr1 175385835 175396165 + --- --- --- --- --- --- ---
+NM_001014974_Ttll4 chr1 74708314 74748400 + --- --- --- --- --- --- ---
+NM_001024721_BC094916 chr1 175451304 175466101 - --- --- --- --- --- --- ---
+NM_001024945_Qsox1 chr1 157625296 157670499 - --- --- --- --- --- --- ---
+NM_001025156_Ccdc93 chr1 123208865 123403037 + --- --- --- --- --- --- ---
+NM_001025565_Lhx9 chr1 140694768 140740509 - --- --- --- --- --- --- ---
+NM_001025602_Il1rl1 chr1 40462708 40522260 + --- --- --- --- --- --- ---
+NM_001029984_Fcrlb chr1 172836813 172843072 - --- --- --- --- --- --- ---
+NM_001037170_Tomm40l chr1 173147934 173152645 - --- --- --- --- --- --- ---
+NM_001037725_Fam117b chr1 59937517 60042190 + --- --- --- --- --- --- ---
+NM_001037918_Lipt1 chr1 37928603 37934232 + --- --- --- --- --- --- ---
+NM_001037999_Dbi chr1 122009883 122046068 - --- --- --- --- --- --- ---
+NM_001038592_Glrx2 chr1 145585774 145608282 + chr1 145591041 145591176 0 5267 . YES
+NM_001038619_Dnm3 chr1 163902671 164408155 - --- --- --- --- --- --- ---
+NM_001039126_Asb1 chr1 93437143 93461729 + --- --- --- --- --- --- ---
+NM_001039472_Kif21b chr1 138027986 138074578 + --- --- --- --- --- --- ---
+NM_001039475_Slco6b1 chr1 98802763 98894139 - --- --- --- --- --- --- ---
+NM_001039482_Klhl20 chr1 163018528 163061699 - --- --- --- --- --- --- ---
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+NM_011283_Rp1 chr1 3989638 4469288 - --- --- --- --- --- --- ---
+NM_011318_Apcs chr1 174824092 174855560 - --- --- --- --- --- --- ---
+NM_011345_Sele chr1 165978323 165988607 + --- --- --- --- --- --- ---
+NM_011346_Sell chr1 165992132 166007817 + --- --- --- --- --- --- ---
+NM_011347_Selp chr1 166045416 166080154 + --- --- --- --- --- --- ---
+NM_011439_Sox13 chr1 135278853 135384763 - --- --- --- --- --- --- ---
+NM_011441_Sox17 chr1 4481009 4487839 - --- --- --- --- --- --- ---
+NM_011459_Serpinb8 chr1 109486542 109586251 + --- --- --- --- --- --- ---
+NM_011465_Spna1 chr1 176102906 176178561 + --- --- --- --- --- --- ---
+NM_011487_Stat4 chr1 52036485 52164030 + --- --- --- --- --- --- ---
+NM_011494_Stk16 chr1 75207414 75212181 + --- --- --- --- --- --- ---
+NM_011541_Tcea1 chr1 4847584 4889703 + --- --- --- --- --- --- ---
+NM_011590_Timm17a chr1 137197272 137210335 - --- --- --- --- --- --- ---
+NM_011633_Traf5 chr1 193821096 193916369 - --- --- --- --- --- --- ---
+NM_011650_Tsn chr1 120194658 120208016 - --- --- --- --- --- --- ---
+NM_011729_Ercc5 chr1 44204270 44256568 + chr1 44195449 44195639 8631 8631 D NO
+NM_011770_Ikzf2 chr1 69574124 69733875 - --- --- --- --- --- --- ---
+NM_011780_Adam23 chr1 63482194 63639230 + --- --- --- --- --- --- ---
+NM_011780_Adam23 chr1 63640970 63642850 + chr1 63664888 63665018 22038 23918 U NO
+NM_011785_Akt3 chr1 178940936 179188314 - --- --- --- --- --- --- ---
+NM_011794_Bpnt1 chr1 187156058 187181696 + --- --- --- --- --- --- ---
+NM_011796_Capn10 chr1 94830953 94844518 + --- --- --- --- --- --- ---
+NM_011800_Cdh20 chr1 106665116 106892058 + --- --- --- --- --- --- ---
+NM_011804_Creg1 chr1 167693878 167710825 + --- --- --- --- --- --- ---
+NM_011811_Farsb chr1 78414533 78506689 - chr1 78630893 78631160 124204 124204 D NO
+NM_011825_Grem2 chr1 176763926 176859770 - --- --- --- --- --- --- ---
+NM_011880_Rgs7 chr1 176989221 177422985 - --- --- --- --- --- --- ---
+NM_011882_Rnasel chr1 155596576 155619417 + --- --- --- --- --- --- ---
+NM_011931_Rfwd2 chr1 161159948 161307408 + --- --- --- --- --- --- ---
+NM_011935_Esrrg chr1 189432683 190062059 + --- --- --- --- --- --- ---
+NM_012009_Sh2d1b1 chr1 172162900 172220030 + --- --- --- --- --- --- ---
+NM_012012_Exo1 chr1 177810732 177841721 + --- --- --- --- --- --- ---
+NM_012049_Nit1 chr1 173270709 173276021 - --- --- --- --- --- --- ---
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+NM_013474_Apoa2 chr1 173151908 173156502 + --- --- --- --- --- --- ---
+NM_013489_Cd84 chr1 173769848 173820852 + --- --- --- --- --- --- ---
+NM_013499_Cr1l chr1 196924298 196957754 - chr1 197057796 197057843 100042 100042 D NO
+NM_013612_Slc11a1 chr1 74421758 74433050 + --- --- --- --- --- --- ---
+NM_013626_Pam chr1 99691711 100053468 - --- --- --- --- --- --- ---
+NM_013673_Sp100 chr1 84943347 87618694 + --- --- --- --- --- --- ---
+NM_013715_Cops5 chr1 10014683 10028315 - --- --- --- --- --- --- ---
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+NM_013784_Pign chr1 107385512 107560244 - --- --- --- --- --- --- ---
+NM_013835_Trove2 chr1 145597816 145624178 - chr1 145591041 145591176 6640 33002 U NO
+NM_013862_Rabgap1l chr1 162149308 162739582 - --- --- --- --- --- --- ---
+NM_013919_Usp21 chr1 173212080 173218102 - --- --- --- --- --- --- ---
+NM_015750_Neu2 chr1 89348720 89494397 + --- --- --- --- --- --- ---
+NM_015780_Cfhr1 chr1 141443639 141456806 - --- --- --- --- --- --- ---
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+NM_015818_Hs6st1 chr1 36125255 36163289 + chr1 36106813 36107058 18197 18197 D NO
+NM_016696_Gpc1 chr1 94728253 94757346 + --- --- --- --- --- --- ---
+NM_016702_Agxt chr1 95031777 95041991 + --- --- --- --- --- --- ---
+NM_016716_Cul3 chr1 80261498 80323399 - --- --- --- --- --- --- ---
+NM_016717_Scly chr1 93192544 93217635 + --- --- --- --- --- --- ---
+NM_016749_Mybph chr1 136090025 136097809 + --- --- --- --- --- --- ---
+NM_016778_Bok chr1 95579016 95592340 + --- --- --- --- --- --- ---
+NM_016796_Vamp4 chr1 164500371 164532593 + --- --- --- --- --- --- ---
+NM_016805_Hnrnpu chr1 180251245 180298730 - --- --- --- --- --- --- ---
+NM_016846_Rgl1 chr1 154357421 154613475 - --- --- --- --- --- --- ---
+NM_016851_Irf6 chr1 194979326 194998230 + chr1 194957396 194957723 21603 21603 D NO
+NM_016894_Ramp1 chr1 93076419 93120251 + --- --- --- --- --- --- ---
+NM_016894_Ramp1 chr1 93120257 93121772 + --- --- --- --- --- --- ---
+NM_016916_Blcap chr1 46068602 46087314 - --- --- --- --- --- --- ---
+NM_016917_Slc40a1 chr1 45964925 45999090 - --- --- --- --- --- --- ---
+NM_016923_Ly96 chr1 16678152 16699618 + --- --- --- --- --- --- ---
+NM_016928_Tlr5 chr1 184884929 184903333 + --- --- --- --- --- --- ---
+NM_016960_Ccl20 chr1 83112527 83138624 + --- --- --- --- --- --- ---
+NM_017480_Icos chr1 61034747 61057162 + --- --- --- --- --- --- ---
+NM_018729_Cd244 chr1 173481630 173515439 + --- --- --- --- --- --- ---
+NM_018750_Rassf5 chr1 133072991 133144761 - chr1 133114860 133115015 0 29746 . YES
+NM_018775_Tbc1d8 chr1 39428350 39544345 - chr1 39492140 39492513 0 51832 . YES
+NM_018796_Eef1b2 chr1 63221360 63227060 + --- --- --- --- --- --- ---
+NM_018817_Smarcal1 chr1 72629842 72679806 + --- --- --- --- --- --- ---
+NM_018868_Nop58 chr1 59741819 59769026 + --- --- --- --- --- --- ---
+NM_018872_Tmem131 chr1 36841788 37000491 - --- --- --- --- --- --- ---
+NM_018881_Fmo2 chr1 164804452 164828875 - --- --- --- --- --- --- ---
+NM_019432_Tmem37 chr1 121962801 121979194 - --- --- --- --- --- --- ---
+NM_019445_Fmn2 chr1 176431685 176752860 + --- --- --- --- --- --- ---
+NM_019479_Hes6 chr1 93308097 93310595 - --- --- --- --- --- --- ---
+NM_019484_Refbp2 chr1 173433397 173434881 + --- --- --- --- --- --- ---
+NM_019562_Uchl5 chr1 145623774 145654586 + chr1 145591041 145591176 32598 32598 D NO
+NM_019570_Rev1 chr1 38109638 38186507 - --- --- --- --- --- --- ---
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+NM_019685_Ruvbl1 chr1 141824644 141826247 - --- --- --- --- --- --- ---
+NM_019759_Dpt chr1 166726785 166754377 + --- --- --- --- --- --- ---
+NM_019777_Ikbke chr1 133151052 133176163 - chr1 133114860 133115015 36037 61148 U NO
+NM_019790_Tmeff2 chr1 50957501 51282275 + --- --- --- --- --- --- ---
+NM_019933_Ptpn4 chr1 121556050 121771541 - --- --- --- --- --- --- ---
+NM_019993_Aldh9a1 chr1 169280142 169298663 + --- --- --- --- --- --- ---
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+NM_020579_B4galt3 chr1 173199650 173207025 + --- --- --- --- --- --- ---
+NM_020588_Tmem183a chr1 136242675 136258707 - --- --- --- --- --- --- ---
+NM_020604_Jph1 chr1 16837549 17087942 - chr1 17030405 17030545 0 57397 . YES
+NM_021285_Myl1 chr1 66948125 66992032 - --- --- --- --- --- --- ---
+NM_021295_Lancl1 chr1 67004053 67085447 - --- --- --- --- --- --- ---
+NM_021306_Ecel1 chr1 89039384 89053076 - --- --- --- --- --- --- ---
+NM_021312_Wdr12 chr1 60099363 60155552 - --- --- --- --- --- --- ---
+NM_021313_Rnf25 chr1 74640329 74648026 - --- --- --- --- --- --- ---
+NM_021342_Kcne4 chr1 78791793 78816579 + --- --- --- --- --- --- ---
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+NM_021374_Rgs20 chr1 4899617 5060346 - --- --- --- --- --- --- ---
+NM_021380_Il20 chr1 132803344 132808275 - --- --- --- --- --- --- ---
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+NM_021400_Prg4 chr1 152296956 152333784 - --- --- --- --- --- --- ---
+NM_021408_Ush2a chr1 190085902 190292167 + --- --- --- --- --- --- ---
+NM_021421_Angel2 chr1 192748297 192770827 + --- --- --- --- --- --- ---
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+NM_021511_Rrs1 chr1 9535513 9537532 + chr1 9619046 9619167 81514 83533 U NO
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+NM_021537_Stk25 chr1 95517348 95555233 - --- --- --- --- --- --- ---
+NM_021541_Cryba2 chr1 74936508 74939802 - --- --- --- --- --- --- ---
+NM_021600_Chrnd chr1 89087192 89096645 + --- --- --- --- --- --- ---
+NM_021605_Nek7 chr1 140379472 140516775 - --- --- --- --- --- --- ---
+NM_021607_Ncstn chr1 173996154 174012927 - --- --- --- --- --- --- ---
+NM_021610_Gpa33 chr1 168060559 168118074 + --- --- --- --- --- --- ---
+NM_022018_Fam129a chr1 153370940 153589282 + --- --- --- --- --- --- ---
+NM_022019_Dusp10 chr1 185755009 185899515 + chr1 185854947 185855105 0 99938 . YES
+NM_022312_Tnr chr1 161327058 161857057 + --- --- --- --- --- --- ---
+NM_022320_Gpr35 chr1 94683531 94882968 + --- --- --- --- --- --- ---
+NM_022327_Ralb chr1 121363651 121401351 - --- --- --- --- --- --- ---
+NM_022329_Ifrg15 chr1 157883344 157900866 + --- --- --- --- --- --- ---
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+NM_022563_Ddr2 chr1 171907607 172040752 - --- --- --- --- --- --- ---
+NM_022721_Fzd5 chr1 64777130 64826549 - --- --- --- --- --- --- ---
+NM_022881_Rgs18 chr1 146599793 146755382 - --- --- --- --- --- --- ---
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+NM_023041_Pex19 chr1 174056859 174067189 + --- --- --- --- --- --- ---
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+NM_023755_Tcfcp2l1 chr1 120524515 120655075 + --- --- --- --- --- --- ---
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+NM_024197_Ndufa10 chr1 94121208 94393553 - --- --- --- --- --- --- ---
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+NM_025303_Stau2 chr1 16218775 16510193 - --- --- --- --- --- --- ---
+NM_025321_Sdhc chr1 173057297 173080736 - --- --- --- --- --- --- ---
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+NM_025424_Nenf chr1 193130454 193141997 - --- --- --- --- --- --- ---
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+NM_026171_Nvl chr1 183008557 183074318 - --- --- --- --- --- --- ---
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+NM_026321_Fam174a chr1 97174825 97346168 + --- --- --- --- --- --- ---
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+NM_026719_Lmbrd1 chr1 24593456 24847969 + chr1 24609562 24609623 0 16106 . YES
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+NM_027725_Wdr69 chr1 83156310 83207145 + --- --- --- --- --- --- ---
+NM_027884_Tns1 chr1 73956820 74144891 - --- --- --- --- --- --- ---
+NM_027886_Stk11ip chr1 75518100 75533910 + chr1 75481920 75482054 36046 36046 D NO
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+NM_028399_Ccnt2 chr1 129670253 129704638 + --- --- --- --- --- --- ---
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+NM_028450_Gulp1 chr1 44608366 44896390 + --- --- --- --- --- --- ---
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+NM_028696_Obfc2a chr1 51417024 51550602 - --- --- --- --- --- --- ---
+NM_028713_Rftn2 chr1 55227030 55283748 - chr1 55283572 55283675 0 73 . YES
+NM_028717_Als2 chr1 59219131 59294111 - --- --- --- --- --- --- ---
+NM_028749_Npl chr1 155350145 155424001 - --- --- --- --- --- --- ---
+NM_028776_Scyl3 chr1 165859251 165885242 + --- --- --- --- --- --- ---
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+NM_028778_Nuak2 chr1 134212715 134241254 + --- --- --- --- --- --- ---
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+NM_028889_Efhd1 chr1 89160561 89207413 + --- --- --- --- --- --- ---
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+NM_029025_Tmem81 chr1 134402623 134405216 + --- --- --- --- --- --- ---
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+NM_029115_4930455F23Rik chr1 166205721 166217973 + --- --- --- --- --- --- ---
+NM_029160_Spag16 chr1 69873526 70771706 + --- --- --- --- --- --- ---
+NM_029269_Spp2 chr1 90303568 90373213 + chr1 90412932 90413132 39719 109364 U NO
+NM_029398_Tmem14a chr1 21143538 21220248 + --- --- --- --- --- --- ---
+NM_029409_Mff chr1 82721393 82748958 + --- --- --- --- --- --- ---
+NM_029612_Slamf9 chr1 174392516 174408706 + chr1 174376470 174376659 15857 15857 D NO
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+NM_029756_Sdccag8 chr1 178743478 178953256 + --- --- --- --- --- --- ---
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+NM_029846_Atg16l1 chr1 89652465 89697344 + --- --- --- --- --- --- ---
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+NM_033570_Cnnm4 chr1 36528452 36565609 + --- --- --- --- --- --- ---
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+NM_176980_Ankar chr1 72689581 72747143 - chr1 72769824 72770056 22681 22681 D NO
+NM_176980_Ankar chr1 72689581 72747143 - chr1 72770058 72770226 22915 22915 D NO
+NM_176980_Ankar chr1 72689581 72747143 - chr1 72815517 72815742 68374 68374 D NO
+NM_177068_Olfml2b chr1 172569075 172612915 + chr1 172620779 172620912 7864 51704 U NO
+NM_177068_Olfml2b chr1 172569075 172612915 + chr1 172620917 172621080 8002 51842 U NO
+NM_177084_Slc9a4 chr1 40636956 40687551 + --- --- --- --- --- --- ---
+NM_177129_Cntn2 chr1 134406005 134442705 - --- --- --- --- --- --- ---
+NM_177164_A830006F12Rik chr1 70772309 70929065 + --- --- --- --- --- --- ---
+NM_177173_A830018L16Rik chr1 11404178 11994163 + --- --- --- --- --- --- ---
+NM_177235_Bend6 chr1 33903283 33964764 - --- --- --- --- --- --- ---
+NM_177243_Slc26a9 chr1 133640599 133668075 + --- --- --- --- --- --- ---
+NM_177305_Arl4c chr1 90569702 90617572 - chr1 90592499 90592629 0 24943 . YES
+NM_177397_Atp6v1g3 chr1 140120875 140186039 + --- --- --- --- --- --- ---
+NM_177445_Dars chr1 130260284 130314013 - --- --- --- --- --- --- ---
+NM_177587_Aqp12 chr1 94886487 94908846 + --- --- --- --- --- --- ---
+NM_177604_AA986860 chr1 132628563 132644539 + --- --- --- --- --- --- ---
+NM_177643_Zfp281 chr1 138487073 138526617 + chr1 138437726 138437860 49213 49213 D NO
+NM_177646_Dgkd chr1 89749836 89841946 + --- --- --- --- --- --- ---
+NM_177722_6030422M02Rik chr1 9898713 9932156 + --- --- --- --- --- --- ---
+NM_177723_Vsig8 chr1 174486069 174513273 + chr1 174376470 174376659 109410 109410 D NO
+NM_177724_D230039L06Rik chr1 180426979 180686112 + --- --- --- --- --- --- ---
+NM_177756_Glt25d2 chr1 154223175 154357825 + --- --- --- --- --- --- ---
+NM_177757_Kif26b chr1 180720593 180862983 + --- --- --- --- --- --- ---
+NM_177781_Trpa1 chr1 14861962 14909072 - --- --- --- --- --- --- ---
+NM_177834_Cpa6 chr1 10314801 10710026 - chr1 10617233 10617437 0 92589 . YES
+NM_177838_Fam163a chr1 157923096 158135544 - --- --- --- --- --- --- ---
+NM_177839_Tnn chr1 161966935 162084477 - --- --- --- --- --- --- ---
+NM_178051_Mterfd2 chr1 95195779 95202630 - chr1 95186508 95186637 9142 15993 U NO
+NM_178055_Dnajb2 chr1 75233016 75242264 + --- --- --- --- --- --- ---
+NM_178119_Agap1 chr1 91351421 91791845 + --- --- --- --- --- --- ---
+NM_178241_Il8ra chr1 74238380 74241205 - --- --- --- --- --- --- ---
+NM_178243_5830403L16Rik chr1 155697272 155747352 - --- --- --- --- --- --- ---
+NM_178244_Teddm1 chr1 155724147 155740188 + --- --- --- --- --- --- ---
+NM_178399_3110035E14Rik chr1 9591248 9617222 + chr1 9619046 9619167 1824 27798 U NO
+NM_178399_3110035E14Rik chr1 9591248 9617222 + chr1 9619175 9619382 1953 27927 U NO
+NM_178405_Atp1a2 chr1 174201852 174233438 - --- --- --- --- --- --- ---
+NM_178593_Rcsd1 chr1 167572007 167639868 - --- --- --- --- --- --- ---
+NM_178598_Tagln2 chr1 174430123 174475991 + chr1 174376470 174376659 53464 53464 D NO
+NM_178601_Imp4 chr1 34496377 34511555 + --- --- --- --- --- --- ---
+NM_178632_Ints7 chr1 193399085 193447550 + --- --- --- --- --- --- ---
+NM_178653_Sccpdh chr1 181598088 181617593 + --- --- --- --- --- --- ---
+NM_178690_Rab3gap1 chr1 129765355 129840723 + --- --- --- --- --- --- ---
+NM_178691_Yod1 chr1 132612680 132618643 + --- --- --- --- --- --- ---
+NM_178692_C130074G19Rik chr1 186695805 186707077 - --- --- --- --- --- --- ---
+NM_178775_Rps6kc1 chr1 192524091 192736016 - --- --- --- --- --- --- ---
+NM_178779_Rnf152 chr1 107176426 107253513 - --- --- --- --- --- --- ---
+NM_178874_Tmcc2 chr1 134252895 134288369 - --- --- --- --- --- --- ---
+NM_178883_Gorab chr1 165315039 165340946 - --- --- --- --- --- --- ---
+NM_178884_Obsl1 chr1 75482401 75503218 - chr1 75481920 75482054 347 21164 U NO
+NM_181405_Rnpepl1 chr1 94807467 94817954 + --- --- --- --- --- --- ---
+NM_181546_Syt14 chr1 194713536 194861959 - chr1 194957396 194957723 95437 95437 D NO
+NM_181750_R3hdm1 chr1 129999892 130134312 + --- --- --- --- --- --- ---
+NM_181796_Gstp2 chr1 193897651 193905509 - --- --- --- --- --- --- ---
+NM_182716_Nfasc chr1 134445291 134638354 - --- --- --- --- --- --- ---
+NM_182930_Plekha6 chr1 135077806 135200008 + --- --- --- --- --- --- ---
+NM_183019_Arhgef4 chr1 34788954 34873560 + --- --- --- --- --- --- ---
+NM_183022_Accn4 chr1 75447063 75470207 + chr1 75481920 75482054 11713 34857 U NO
+NM_183027_Ap1s3 chr1 79591820 79668545 - --- --- --- --- --- --- ---
+NM_183028_Pcmtd1 chr1 7079053 7163709 + --- --- --- --- --- --- ---
+NM_183124_Defb41 chr1 18241071 18350659 - --- --- --- --- --- --- ---
+NM_183355_Pbx1 chr1 170049495 170512777 - --- --- --- --- --- --- ---
+NM_183391_Tnfsf18 chr1 163373523 163524094 + --- --- --- --- --- --- ---
+NM_194333_Slc23a3 chr1 75120731 75130464 - --- --- --- --- --- --- ---
+NM_198006_6330578E17Rik chr1 37473934 37474944 - --- --- --- --- --- --- ---
+NM_198006_6330578E17Rik chr1 37477057 37486928 - --- --- --- --- --- --- ---
+NM_198028_Serpinb10 chr1 109425580 109445838 + --- --- --- --- --- --- ---
+NM_198127_Abi2 chr1 60466022 60537998 + --- --- --- --- --- --- ---
+NM_198247_Sertad4 chr1 194670313 194693726 - chr1 194645118 194645475 24838 48251 U NO
+NM_198303_Eif5b chr1 38054627 38112414 + --- --- --- --- --- --- ---
+NM_198652_6430706D22Rik chr1 90158880 90174174 - --- --- --- --- --- --- ---
+NM_198653_Iars2 chr1 187109458 187153280 - --- --- --- --- --- --- ---
+NM_198654_Nsl1 chr1 192886918 192919389 + --- --- --- --- --- --- ---
+NM_198680_Serpinb3b chr1 109033488 109059720 - --- --- --- --- --- --- ---
+NM_198899_Ugcgl1 chr1 36196873 36301555 - --- --- --- --- --- --- ---
+NM_198934_Pou2f1 chr1 167804181 167932753 - chr1 167906284 167906554 0 26199 . YES
+NM_199007_Sgol2 chr1 58026657 58085164 + --- --- --- --- --- --- ---
+NM_199021_Dpp10 chr1 125044486 126749525 - --- --- --- --- --- --- ---
+NM_201363_Serpinb3c chr1 109088051 109198931 - --- --- --- --- --- --- ---
+NM_201376_Serpinb3d chr1 108974770 108980057 - --- --- --- --- --- --- ---
+NM_201641_Ugt1a10 chr1 89922380 90115570 + chr1 89989553 89989714 0 67173 . YES
+NM_206896_Olfr12 chr1 94516341 94538591 + --- --- --- --- --- --- ---
+NM_207031_Ano7 chr1 95270385 95302271 + chr1 95186508 95186637 83748 83748 D NO
+NM_207137_Olfr417 chr1 176299050 176299979 + --- --- --- --- --- --- ---
+NM_207137_Olfr417 chr1 176321202 176322113 + --- --- --- --- --- --- ---
+NM_207158_Olfr427 chr1 176028781 176030538 + --- --- --- --- --- --- ---
+NM_207225_Hdac4 chr1 93755950 94103099 - --- --- --- --- --- --- ---
+NM_207228_Tsga10 chr1 37783457 37922148 - --- --- --- --- --- --- ---
+NM_207233_C1ql2 chr1 122196386 122239751 + --- --- --- --- --- --- ---
+NM_207281_4832428D23Rik chr1 44260915 44515719 - --- --- --- --- --- --- ---
+NM_207583_Fam5b chr1 160175402 160286644 - --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58768296 58813658 + --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58813703 58815725 + --- --- --- --- --- --- ---
+NM_213616_Atp2b4 chr1 135602265 135697538 - chr1 135582677 135582828 19437 114710 U NO
+NR_002840_Gas5 chr1 162964758 162968663 + --- --- --- --- --- --- ---
+NR_002858_EG241041 chr1 21268965 21306401 - --- --- --- --- --- --- ---
+NR_002870_Dnm3os chr1 164119785 164155671 + chr1 164215623 164215935 59952 95838 U NO
+NR_003623_EG277333 chr1 182251970 182262902 - --- --- --- --- --- --- ---
+NR_026896_4931440L10Rik chr1 136437533 136449760 - --- --- --- --- --- --- ---
diff -r 000000000000 -r 0abe6bac47a6 test-data/peaks_per_feature3.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peaks_per_feature3.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,30 @@
+#gene.id gene.chr gene.start gene.end gene.strand chr_1 start_1 end_1 dist_closest_1 dist_TSS_1 direction_1 in_the_gene_1 chr_2 start_2 end_2 dist_closest_2 dist_TSS_2 direction_2 in_the_gene_2 chr_3 start_3 end_3 dist_closest_3 dist_TSS_3 direction_3 in_the_gene_3 chr_4 start_4 end_4 dist_closest_4 dist_TSS_4 direction_4 in_the_gene_4
+AF064749_Col6a3 chr1 92566771 92800755 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK015559_4930472D16Rik chr1 25020851 25021989 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK030377_A330023F24Rik chr1 196781953 196826186 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK080193_A530079E22Rik chr1 89401837 89403491 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK082264_C230030N03Rik chr1 34735043 34781084 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC006931_AI597479 chr1 43153807 43172843 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC021773_Glb1l chr1 75193364 75207353 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC023951_D1Ertd622e chr1 99540054 99558631 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC028767_3110009E18Rik chr1 122017764 122114603 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC031781_BC031781 chr1 182781250 182798240 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC034187_BC035947 chr1 78493611 78497758 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC043098_Fam168b chr1 34870072 34917183 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC049091_D1Bwg0212e chr1 39592545 39603734 + chr1 39492140 39492513 100032 100032 D NO . . . . . . . . . . . . . . . . . . . . .
+BC049713_Ankrd45 chr1 163072817 163099826 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC050813_4921511C04Rik chr1 37157481 37244861 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC051128_4921521F21Rik chr1 65059273 65079312 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC052693_2810422O20Rik chr1 165924541 165927371 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC052931_A630001G21Rik chr1 87601462 87674840 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC053100_5730559C18Rik chr1 138110108 138130841 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC054802_9630058J23Rik chr1 181476521 181558044 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC055845_2810025M15Rik chr1 159342483 159350353 + chr1 159240736 159240866 101617 101617 D NO . . . . . . . . . . . . . . . . . . . . .
+BC055955_A130010J15Rik chr1 194999663 195004015 + chr1 194957396 194957723 41940 41940 D NO . . . . . . . . . . . . . . . . . . . . .
+BC057872_Rab3gap2 chr1 187028006 187110623 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC058417_2610017I09Rik chr1 42648822 42751667 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC059254_Phlpp chr1 108042052 108306367 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC070435_Fam123c chr1 34620070 34671545 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC070446_Fam135a chr1 24017617 24107170 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC071241_9430016H08Rik chr1 57463192 57497936 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC072639_2010300C02Rik chr1 37646877 37776659 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
diff -r 000000000000 -r 0abe6bac47a6 test-data/peaks_per_feature4.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peaks_per_feature4.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,3825 @@
+#gene.id gene.chr gene.start gene.end gene.strand chr start end dist_closest dist_TSS direction in_the_gene
+AF064749_Col6a3 chr1 92566771 92800755 - --- --- --- --- --- --- ---
+AF064749_Col6a3 chr1 92566771 92800755 - --- --- --- --- --- --- ---
+AF064749_Col6a3 chr1 92566771 92800755 - --- --- --- --- --- --- ---
+AF064749_Col6a3 chr1 92566771 92800755 - --- --- --- --- --- --- ---
+AK015559_4930472D16Rik chr1 25020851 25021989 - --- --- --- --- --- --- ---
+AK015559_4930472D16Rik chr1 25020851 25021989 - --- --- --- --- --- --- ---
+AK015559_4930472D16Rik chr1 25020851 25021989 - --- --- --- --- --- --- ---
+AK015559_4930472D16Rik chr1 25020851 25021989 - --- --- --- --- --- --- ---
+AK030377_A330023F24Rik chr1 196781953 196826186 - --- --- --- --- --- --- ---
+AK030377_A330023F24Rik chr1 196781953 196826186 - --- --- --- --- --- --- ---
+AK030377_A330023F24Rik chr1 196781953 196826186 - --- --- --- --- --- --- ---
+AK030377_A330023F24Rik chr1 196781953 196826186 - --- --- --- --- --- --- ---
+AK080193_A530079E22Rik chr1 89401837 89403491 - --- --- --- --- --- --- ---
+AK080193_A530079E22Rik chr1 89401837 89403491 - --- --- --- --- --- --- ---
+AK080193_A530079E22Rik chr1 89401837 89403491 - --- --- --- --- --- --- ---
+AK080193_A530079E22Rik chr1 89401837 89403491 - --- --- --- --- --- --- ---
+AK082264_C230030N03Rik chr1 34735043 34781084 + --- --- --- --- --- --- ---
+AK082264_C230030N03Rik chr1 34735043 34781084 + --- --- --- --- --- --- ---
+AK082264_C230030N03Rik chr1 34735043 34781084 + --- --- --- --- --- --- ---
+AK082264_C230030N03Rik chr1 34735043 34781084 + --- --- --- --- --- --- ---
+BC006931_AI597479 chr1 43153807 43172843 + --- --- --- --- --- --- ---
+BC006931_AI597479 chr1 43153807 43172843 + --- --- --- --- --- --- ---
+BC006931_AI597479 chr1 43153807 43172843 + --- --- --- --- --- --- ---
+BC006931_AI597479 chr1 43153807 43172843 + --- --- --- --- --- --- ---
+BC021773_Glb1l chr1 75193364 75207353 - --- --- --- --- --- --- ---
+BC021773_Glb1l chr1 75193364 75207353 - --- --- --- --- --- --- ---
+BC021773_Glb1l chr1 75193364 75207353 - --- --- --- --- --- --- ---
+BC021773_Glb1l chr1 75193364 75207353 - --- --- --- --- --- --- ---
+BC023951_D1Ertd622e chr1 99540054 99558631 - --- --- --- --- --- --- ---
+BC023951_D1Ertd622e chr1 99540054 99558631 - --- --- --- --- --- --- ---
+BC023951_D1Ertd622e chr1 99540054 99558631 - --- --- --- --- --- --- ---
+BC023951_D1Ertd622e chr1 99540054 99558631 - --- --- --- --- --- --- ---
+BC028767_3110009E18Rik chr1 122017764 122114603 + --- --- --- --- --- --- ---
+BC028767_3110009E18Rik chr1 122017764 122114603 + --- --- --- --- --- --- ---
+BC028767_3110009E18Rik chr1 122017764 122114603 + --- --- --- --- --- --- ---
+BC028767_3110009E18Rik chr1 122017764 122114603 + --- --- --- --- --- --- ---
+BC031781_BC031781 chr1 182781250 182798240 + --- --- --- --- --- --- ---
+BC031781_BC031781 chr1 182781250 182798240 + --- --- --- --- --- --- ---
+BC031781_BC031781 chr1 182781250 182798240 + --- --- --- --- --- --- ---
+BC031781_BC031781 chr1 182781250 182798240 + --- --- --- --- --- --- ---
+BC034187_BC035947 chr1 78493611 78497758 - --- --- --- --- --- --- ---
+BC034187_BC035947 chr1 78493611 78497758 - --- --- --- --- --- --- ---
+BC034187_BC035947 chr1 78493611 78497758 - --- --- --- --- --- --- ---
+BC034187_BC035947 chr1 78493611 78497758 - --- --- --- --- --- --- ---
+BC043098_Fam168b chr1 34870072 34917183 - --- --- --- --- --- --- ---
+BC043098_Fam168b chr1 34870072 34917183 - --- --- --- --- --- --- ---
+BC043098_Fam168b chr1 34870072 34917183 - --- --- --- --- --- --- ---
+BC043098_Fam168b chr1 34870072 34917183 - --- --- --- --- --- --- ---
+BC049091_D1Bwg0212e chr1 39592545 39603734 + chr1 39492140 39492513 100032 100032 D NO
+BC049091_D1Bwg0212e chr1 39592545 39603734 + --- --- --- --- --- --- ---
+BC049091_D1Bwg0212e chr1 39592545 39603734 + --- --- --- --- --- --- ---
+BC049091_D1Bwg0212e chr1 39592545 39603734 + --- --- --- --- --- --- ---
+BC049713_Ankrd45 chr1 163072817 163099826 + --- --- --- --- --- --- ---
+BC049713_Ankrd45 chr1 163072817 163099826 + --- --- --- --- --- --- ---
+BC049713_Ankrd45 chr1 163072817 163099826 + --- --- --- --- --- --- ---
+BC049713_Ankrd45 chr1 163072817 163099826 + --- --- --- --- --- --- ---
+BC050813_4921511C04Rik chr1 37157481 37244861 + --- --- --- --- --- --- ---
+BC050813_4921511C04Rik chr1 37157481 37244861 + --- --- --- --- --- --- ---
+BC050813_4921511C04Rik chr1 37157481 37244861 + --- --- --- --- --- --- ---
+BC050813_4921511C04Rik chr1 37157481 37244861 + --- --- --- --- --- --- ---
+BC051128_4921521F21Rik chr1 65059273 65079312 - --- --- --- --- --- --- ---
+BC051128_4921521F21Rik chr1 65059273 65079312 - --- --- --- --- --- --- ---
+BC051128_4921521F21Rik chr1 65059273 65079312 - --- --- --- --- --- --- ---
+BC051128_4921521F21Rik chr1 65059273 65079312 - --- --- --- --- --- --- ---
+BC052693_2810422O20Rik chr1 165924541 165927371 + --- --- --- --- --- --- ---
+BC052693_2810422O20Rik chr1 165924541 165927371 + --- --- --- --- --- --- ---
+BC052693_2810422O20Rik chr1 165924541 165927371 + --- --- --- --- --- --- ---
+BC052693_2810422O20Rik chr1 165924541 165927371 + --- --- --- --- --- --- ---
+BC052931_A630001G21Rik chr1 87601462 87674840 - --- --- --- --- --- --- ---
+BC052931_A630001G21Rik chr1 87601462 87674840 - --- --- --- --- --- --- ---
+BC052931_A630001G21Rik chr1 87601462 87674840 - --- --- --- --- --- --- ---
+BC052931_A630001G21Rik chr1 87601462 87674840 - --- --- --- --- --- --- ---
+BC053100_5730559C18Rik chr1 138110108 138130841 - --- --- --- --- --- --- ---
+BC053100_5730559C18Rik chr1 138110108 138130841 - --- --- --- --- --- --- ---
+BC053100_5730559C18Rik chr1 138110108 138130841 - --- --- --- --- --- --- ---
+BC053100_5730559C18Rik chr1 138110108 138130841 - --- --- --- --- --- --- ---
+BC054802_9630058J23Rik chr1 181476521 181558044 + --- --- --- --- --- --- ---
+BC054802_9630058J23Rik chr1 181476521 181558044 + --- --- --- --- --- --- ---
+BC054802_9630058J23Rik chr1 181476521 181558044 + --- --- --- --- --- --- ---
+BC054802_9630058J23Rik chr1 181476521 181558044 + --- --- --- --- --- --- ---
+BC055845_2810025M15Rik chr1 159342483 159350353 + chr1 159240736 159240866 101617 101617 D NO
+BC055845_2810025M15Rik chr1 159342483 159350353 + --- --- --- --- --- --- ---
+BC055845_2810025M15Rik chr1 159342483 159350353 + --- --- --- --- --- --- ---
+BC055845_2810025M15Rik chr1 159342483 159350353 + --- --- --- --- --- --- ---
+BC055955_A130010J15Rik chr1 194999663 195004015 + chr1 194957396 194957723 41940 41940 D NO
+BC055955_A130010J15Rik chr1 194999663 195004015 + --- --- --- --- --- --- ---
+BC055955_A130010J15Rik chr1 194999663 195004015 + --- --- --- --- --- --- ---
+BC055955_A130010J15Rik chr1 194999663 195004015 + --- --- --- --- --- --- ---
+BC057872_Rab3gap2 chr1 187028006 187110623 + --- --- --- --- --- --- ---
+BC057872_Rab3gap2 chr1 187028006 187110623 + --- --- --- --- --- --- ---
+BC057872_Rab3gap2 chr1 187028006 187110623 + --- --- --- --- --- --- ---
+BC057872_Rab3gap2 chr1 187028006 187110623 + --- --- --- --- --- --- ---
+BC058417_2610017I09Rik chr1 42648822 42751667 - --- --- --- --- --- --- ---
+BC058417_2610017I09Rik chr1 42648822 42751667 - --- --- --- --- --- --- ---
+BC058417_2610017I09Rik chr1 42648822 42751667 - --- --- --- --- --- --- ---
+BC058417_2610017I09Rik chr1 42648822 42751667 - --- --- --- --- --- --- ---
+BC059254_Phlpp chr1 108042052 108306367 + --- --- --- --- --- --- ---
+BC059254_Phlpp chr1 108042052 108306367 + --- --- --- --- --- --- ---
+BC059254_Phlpp chr1 108042052 108306367 + --- --- --- --- --- --- ---
+BC059254_Phlpp chr1 108042052 108306367 + --- --- --- --- --- --- ---
+BC070435_Fam123c chr1 34620070 34671545 + --- --- --- --- --- --- ---
+BC070435_Fam123c chr1 34620070 34671545 + --- --- --- --- --- --- ---
+BC070435_Fam123c chr1 34620070 34671545 + --- --- --- --- --- --- ---
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+NM_010267_Gdap1 chr1 17135463 17385513 + --- --- --- --- --- --- ---
+NM_010267_Gdap1 chr1 17135463 17385513 + --- --- --- --- --- --- ---
+NM_010341_Nmur1 chr1 88282479 88297441 - chr1 88408969 88409267 111528 111528 D NO
+NM_010341_Nmur1 chr1 88282479 88297441 - --- --- --- --- --- --- ---
+NM_010341_Nmur1 chr1 88282479 88297441 - --- --- --- --- --- --- ---
+NM_010341_Nmur1 chr1 88282479 88297441 - --- --- --- --- --- --- ---
+NM_010472_Agfg1 chr1 82836048 82918151 + --- --- --- --- --- --- ---
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+NM_010476_Hsd17b7 chr1 171879671 171899542 - --- --- --- --- --- --- ---
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+NM_010483_Htr5b chr1 123406263 123425032 - --- --- --- --- --- --- ---
+NM_010483_Htr5b chr1 123406263 123425032 - --- --- --- --- --- --- ---
+NM_010483_Htr5b chr1 123406263 123425032 - --- --- --- --- --- --- ---
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+NM_010518_Igfbp5 chr1 72904507 72921468 - chr1 72815517 72815742 88765 105726 U NO
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+NM_010518_Igfbp5 chr1 72904507 72921468 - --- --- --- --- --- --- ---
+NM_010544_Ihh chr1 74991633 75093213 - --- --- --- --- --- --- ---
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+NM_010548_Il10 chr1 132916424 132921547 + chr1 132950929 132951247 29382 34505 U NO
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+NM_010564_Inha chr1 75503647 75506924 + chr1 75481920 75482054 21593 21593 D NO
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+NM_010607_Kcnk2 chr1 191031813 191229415 - --- --- --- --- --- --- ---
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+NM_010629_Kifap3 chr1 165671988 165847216 + --- --- --- --- --- --- ---
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+NM_010678_Aff3 chr1 38232856 38782360 - --- --- --- --- --- --- ---
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+NM_010683_Lamc1 chr1 155065803 155179906 - chr1 155123313 155123435 0 56471 . YES
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+NM_010683_Lamc1 chr1 155065803 155179906 - --- --- --- --- --- --- ---
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+NM_010766_Marco chr1 122261022 122466383 - --- --- --- --- --- --- ---
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+NM_010766_Marco chr1 122261022 122466383 - --- --- --- --- --- --- ---
+NM_010778_Cd46 chr1 196861976 196919007 - --- --- --- --- --- --- ---
+NM_010778_Cd46 chr1 196861976 196919007 - --- --- --- --- --- --- ---
+NM_010778_Cd46 chr1 196861976 196919007 - --- --- --- --- --- --- ---
+NM_010778_Cd46 chr1 196861976 196919007 - --- --- --- --- --- --- ---
+NM_010827_Msc chr1 14520272 14746075 - --- --- --- --- --- --- ---
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+NM_011729_Ercc5 chr1 44204270 44256568 + chr1 44195449 44195639 8631 8631 D NO
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+NM_011780_Adam23 chr1 63640970 63642850 + chr1 63664888 63665018 22038 23918 U NO
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+NM_011794_Bpnt1 chr1 187156058 187181696 + --- --- --- --- --- --- ---
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+NM_019790_Tmeff2 chr1 50957501 51282275 + --- --- --- --- --- --- ---
+NM_019933_Ptpn4 chr1 121556050 121771541 - --- --- --- --- --- --- ---
+NM_019933_Ptpn4 chr1 121556050 121771541 - --- --- --- --- --- --- ---
+NM_019933_Ptpn4 chr1 121556050 121771541 - --- --- --- --- --- --- ---
+NM_019933_Ptpn4 chr1 121556050 121771541 - --- --- --- --- --- --- ---
+NM_019993_Aldh9a1 chr1 169280142 169298663 + --- --- --- --- --- --- ---
+NM_019993_Aldh9a1 chr1 169280142 169298663 + --- --- --- --- --- --- ---
+NM_019993_Aldh9a1 chr1 169280142 169298663 + --- --- --- --- --- --- ---
+NM_019993_Aldh9a1 chr1 169280142 169298663 + --- --- --- --- --- --- ---
+NM_020025_B3galt2 chr1 145487786 145497516 + chr1 145591041 145591176 93525 103255 U NO
+NM_020025_B3galt2 chr1 145487786 145497516 + --- --- --- --- --- --- ---
+NM_020025_B3galt2 chr1 145487786 145497516 + --- --- --- --- --- --- ---
+NM_020025_B3galt2 chr1 145487786 145497516 + --- --- --- --- --- --- ---
+NM_020579_B4galt3 chr1 173199650 173207025 + --- --- --- --- --- --- ---
+NM_020579_B4galt3 chr1 173199650 173207025 + --- --- --- --- --- --- ---
+NM_020579_B4galt3 chr1 173199650 173207025 + --- --- --- --- --- --- ---
+NM_020579_B4galt3 chr1 173199650 173207025 + --- --- --- --- --- --- ---
+NM_020588_Tmem183a chr1 136242675 136258707 - --- --- --- --- --- --- ---
+NM_020588_Tmem183a chr1 136242675 136258707 - --- --- --- --- --- --- ---
+NM_020588_Tmem183a chr1 136242675 136258707 - --- --- --- --- --- --- ---
+NM_020588_Tmem183a chr1 136242675 136258707 - --- --- --- --- --- --- ---
+NM_020604_Jph1 chr1 16837549 17087942 - chr1 17030405 17030545 0 57397 . YES
+NM_020604_Jph1 chr1 16837549 17087942 - --- --- --- --- --- --- ---
+NM_020604_Jph1 chr1 16837549 17087942 - --- --- --- --- --- --- ---
+NM_020604_Jph1 chr1 16837549 17087942 - --- --- --- --- --- --- ---
+NM_021285_Myl1 chr1 66948125 66992032 - --- --- --- --- --- --- ---
+NM_021285_Myl1 chr1 66948125 66992032 - --- --- --- --- --- --- ---
+NM_021285_Myl1 chr1 66948125 66992032 - --- --- --- --- --- --- ---
+NM_021285_Myl1 chr1 66948125 66992032 - --- --- --- --- --- --- ---
+NM_021295_Lancl1 chr1 67004053 67085447 - --- --- --- --- --- --- ---
+NM_021295_Lancl1 chr1 67004053 67085447 - --- --- --- --- --- --- ---
+NM_021295_Lancl1 chr1 67004053 67085447 - --- --- --- --- --- --- ---
+NM_021295_Lancl1 chr1 67004053 67085447 - --- --- --- --- --- --- ---
+NM_021306_Ecel1 chr1 89039384 89053076 - --- --- --- --- --- --- ---
+NM_021306_Ecel1 chr1 89039384 89053076 - --- --- --- --- --- --- ---
+NM_021306_Ecel1 chr1 89039384 89053076 - --- --- --- --- --- --- ---
+NM_021306_Ecel1 chr1 89039384 89053076 - --- --- --- --- --- --- ---
+NM_021312_Wdr12 chr1 60099363 60155552 - --- --- --- --- --- --- ---
+NM_021312_Wdr12 chr1 60099363 60155552 - --- --- --- --- --- --- ---
+NM_021312_Wdr12 chr1 60099363 60155552 - --- --- --- --- --- --- ---
+NM_021312_Wdr12 chr1 60099363 60155552 - --- --- --- --- --- --- ---
+NM_021313_Rnf25 chr1 74640329 74648026 - --- --- --- --- --- --- ---
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+NM_021313_Rnf25 chr1 74640329 74648026 - --- --- --- --- --- --- ---
+NM_021313_Rnf25 chr1 74640329 74648026 - --- --- --- --- --- --- ---
+NM_021342_Kcne4 chr1 78791793 78816579 + --- --- --- --- --- --- ---
+NM_021342_Kcne4 chr1 78791793 78816579 + --- --- --- --- --- --- ---
+NM_021342_Kcne4 chr1 78791793 78816579 + --- --- --- --- --- --- ---
+NM_021342_Kcne4 chr1 78791793 78816579 + --- --- --- --- --- --- ---
+NM_021350_Chml chr1 177615948 177618649 - --- --- --- --- --- --- ---
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+NM_021350_Chml chr1 177615948 177618649 - --- --- --- --- --- --- ---
+NM_021350_Chml chr1 177615948 177618649 - --- --- --- --- --- --- ---
+NM_021374_Rgs20 chr1 4899617 5060346 - --- --- --- --- --- --- ---
+NM_021374_Rgs20 chr1 4899617 5060346 - --- --- --- --- --- --- ---
+NM_021374_Rgs20 chr1 4899617 5060346 - --- --- --- --- --- --- ---
+NM_021374_Rgs20 chr1 4899617 5060346 - --- --- --- --- --- --- ---
+NM_021380_Il20 chr1 132803344 132808275 - --- --- --- --- --- --- ---
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+NM_021380_Il20 chr1 132803344 132808275 - --- --- --- --- --- --- ---
+NM_021380_Il20 chr1 132803344 132808275 - --- --- --- --- --- --- ---
+NM_021383_Rqcd1 chr1 74542393 74577404 + --- --- --- --- --- --- ---
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+NM_021383_Rqcd1 chr1 74542393 74577404 + --- --- --- --- --- --- ---
+NM_021400_Prg4 chr1 152296956 152333784 - --- --- --- --- --- --- ---
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+NM_021400_Prg4 chr1 152296956 152333784 - --- --- --- --- --- --- ---
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+NM_021408_Ush2a chr1 190085902 190292167 + --- --- --- --- --- --- ---
+NM_021408_Ush2a chr1 190085902 190292167 + --- --- --- --- --- --- ---
+NM_021408_Ush2a chr1 190085902 190292167 + --- --- --- --- --- --- ---
+NM_021408_Ush2a chr1 190085902 190292167 + --- --- --- --- --- --- ---
+NM_021421_Angel2 chr1 192748297 192770827 + --- --- --- --- --- --- ---
+NM_021421_Angel2 chr1 192748297 192770827 + --- --- --- --- --- --- ---
+NM_021421_Angel2 chr1 192748297 192770827 + --- --- --- --- --- --- ---
+NM_021421_Angel2 chr1 192748297 192770827 + --- --- --- --- --- --- ---
+NM_021433_Stx6 chr1 157005819 157054716 + --- --- --- --- --- --- ---
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+NM_021433_Stx6 chr1 157005819 157054716 + --- --- --- --- --- --- ---
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+NM_021467_Tnni1 chr1 137676021 137713725 + --- --- --- --- --- --- ---
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+NM_021467_Tnni1 chr1 137676021 137713725 + --- --- --- --- --- --- ---
+NM_021467_Tnni1 chr1 137676021 137713725 + --- --- --- --- --- --- ---
+NM_021511_Rrs1 chr1 9535513 9537532 + chr1 9619046 9619167 81514 83533 U NO
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+NM_021511_Rrs1 chr1 9535513 9537532 + --- --- --- --- --- --- ---
+NM_021511_Rrs1 chr1 9535513 9537532 + --- --- --- --- --- --- ---
+NM_021537_Stk25 chr1 95517348 95555233 - --- --- --- --- --- --- ---
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+NM_021537_Stk25 chr1 95517348 95555233 - --- --- --- --- --- --- ---
+NM_021541_Cryba2 chr1 74936508 74939802 - --- --- --- --- --- --- ---
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+NM_021541_Cryba2 chr1 74936508 74939802 - --- --- --- --- --- --- ---
+NM_021600_Chrnd chr1 89087192 89096645 + --- --- --- --- --- --- ---
+NM_021600_Chrnd chr1 89087192 89096645 + --- --- --- --- --- --- ---
+NM_021600_Chrnd chr1 89087192 89096645 + --- --- --- --- --- --- ---
+NM_021600_Chrnd chr1 89087192 89096645 + --- --- --- --- --- --- ---
+NM_021605_Nek7 chr1 140379472 140516775 - --- --- --- --- --- --- ---
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+NM_021607_Ncstn chr1 173996154 174012927 - --- --- --- --- --- --- ---
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+NM_021607_Ncstn chr1 173996154 174012927 - --- --- --- --- --- --- ---
+NM_021610_Gpa33 chr1 168060559 168118074 + --- --- --- --- --- --- ---
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+NM_021610_Gpa33 chr1 168060559 168118074 + --- --- --- --- --- --- ---
+NM_022018_Fam129a chr1 153370940 153589282 + --- --- --- --- --- --- ---
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+NM_022018_Fam129a chr1 153370940 153589282 + --- --- --- --- --- --- ---
+NM_022019_Dusp10 chr1 185755009 185899515 + chr1 185854947 185855105 0 99938 . YES
+NM_022019_Dusp10 chr1 185755009 185899515 + --- --- --- --- --- --- ---
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+NM_022312_Tnr chr1 161327058 161857057 + --- --- --- --- --- --- ---
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+NM_022320_Gpr35 chr1 94683531 94882968 + --- --- --- --- --- --- ---
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+NM_022327_Ralb chr1 121363651 121401351 - --- --- --- --- --- --- ---
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+NM_022329_Ifrg15 chr1 157883344 157900866 + --- --- --- --- --- --- ---
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+NM_022417_Itm2c chr1 87780787 87838221 + --- --- --- --- --- --- ---
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+NM_022721_Fzd5 chr1 64777130 64826549 - --- --- --- --- --- --- ---
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+NM_022881_Rgs18 chr1 146599793 146755382 - --- --- --- --- --- --- ---
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+NM_022988_Nif3l1 chr1 58501750 58538650 + --- --- --- --- --- --- ---
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+NM_023041_Pex19 chr1 174056859 174067189 + --- --- --- --- --- --- ---
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+NM_023200_Ppp1r7 chr1 95239431 95266345 + chr1 95186508 95186637 52794 52794 D NO
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+NM_023200_Ppp1r7 chr1 95239431 95266345 + --- --- --- --- --- --- ---
+NM_023284_Nuf2 chr1 171386224 171461676 - --- --- --- --- --- --- ---
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+NM_023314_Eif4e2 chr1 89110486 89145136 + --- --- --- --- --- --- ---
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+NM_023341_Cabc1 chr1 182095369 182129713 - --- --- --- --- --- --- ---
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+NM_023343_Ilkap chr1 93270445 93290447 - --- --- --- --- --- --- ---
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+NM_023343_Ilkap chr1 93270445 93290447 - --- --- --- --- --- --- ---
+NM_023434_Tox4 chr1 16757104 16760219 - --- --- --- --- --- --- ---
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+NM_023514_Mrps9 chr1 42760822 42962528 + --- --- --- --- --- --- ---
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+NM_023645_Kdelc1 chr1 44143458 44177102 - chr1 44195449 44195639 18347 18347 D NO
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+NM_023645_Kdelc1 chr1 44143458 44177102 - --- --- --- --- --- --- ---
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+NM_023884_Ralgps2 chr1 158734300 158969600 - --- --- --- --- --- --- ---
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+NM_024197_Ndufa10 chr1 94121208 94393553 - --- --- --- --- --- --- ---
+NM_024264_Cyp27a1 chr1 74759770 74786412 + --- --- --- --- --- --- ---
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+NM_024283_1500015O10Rik chr1 43787414 43799399 + --- --- --- --- --- --- ---
+NM_025283_Mobkl3 chr1 55187734 55211736 + chr1 55283572 55283675 71836 95838 U NO
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+NM_025283_Mobkl3 chr1 55187734 55211736 + --- --- --- --- --- --- ---
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+NM_025300_Mrpl15 chr1 4763290 4798011 - --- --- --- --- --- --- ---
+NM_025300_Mrpl15 chr1 4763290 4798011 - --- --- --- --- --- --- ---
+NM_025300_Mrpl15 chr1 4763290 4798011 - --- --- --- --- --- --- ---
+NM_025303_Stau2 chr1 16218775 16510193 - --- --- --- --- --- --- ---
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+NM_025303_Stau2 chr1 16218775 16510193 - --- --- --- --- --- --- ---
+NM_025321_Sdhc chr1 173057297 173080736 - --- --- --- --- --- --- ---
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+NM_025321_Sdhc chr1 173057297 173080736 - --- --- --- --- --- --- ---
+NM_025386_Fbxo36 chr1 84835492 84897059 + --- --- --- --- --- --- ---
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+NM_025386_Fbxo36 chr1 84835492 84897059 + --- --- --- --- --- --- ---
+NM_025388_Ufc1 chr1 173218698 173225135 - --- --- --- --- --- --- ---
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+NM_025388_Ufc1 chr1 173218698 173225135 - --- --- --- --- --- --- ---
+NM_025388_Ufc1 chr1 173218698 173225135 - --- --- --- --- --- --- ---
+NM_025424_Nenf chr1 193130454 193141997 - --- --- --- --- --- --- ---
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+NM_025424_Nenf chr1 193130454 193141997 - --- --- --- --- --- --- ---
+NM_025424_Nenf chr1 193130454 193141997 - --- --- --- --- --- --- ---
+NM_025439_Tmem9 chr1 137879942 137931919 + --- --- --- --- --- --- ---
+NM_025439_Tmem9 chr1 137879942 137931919 + --- --- --- --- --- --- ---
+NM_025439_Tmem9 chr1 137879942 137931919 + --- --- --- --- --- --- ---
+NM_025439_Tmem9 chr1 137879942 137931919 + --- --- --- --- --- --- ---
+NM_025453_Tm4sf20 chr1 82749860 82765031 - --- --- --- --- --- --- ---
+NM_025453_Tm4sf20 chr1 82749860 82765031 - --- --- --- --- --- --- ---
+NM_025453_Tm4sf20 chr1 82749860 82765031 - --- --- --- --- --- --- ---
+NM_025453_Tm4sf20 chr1 82749860 82765031 - --- --- --- --- --- --- ---
+NM_025454_Ing5 chr1 95700534 95719794 + --- --- --- --- --- --- ---
+NM_025454_Ing5 chr1 95700534 95719794 + --- --- --- --- --- --- ---
+NM_025454_Ing5 chr1 95700534 95719794 + --- --- --- --- --- --- ---
+NM_025454_Ing5 chr1 95700534 95719794 + --- --- --- --- --- --- ---
+NM_025470_1810030J14Rik chr1 176260650 176349219 + --- --- --- --- --- --- ---
+NM_025470_1810030J14Rik chr1 176260650 176349219 + --- --- --- --- --- --- ---
+NM_025470_1810030J14Rik chr1 176260650 176349219 + --- --- --- --- --- --- ---
+NM_025470_1810030J14Rik chr1 176260650 176349219 + --- --- --- --- --- --- ---
+NM_025474_Mrps14 chr1 162082365 162131317 + --- --- --- --- --- --- ---
+NM_025474_Mrps14 chr1 162082365 162131317 + --- --- --- --- --- --- ---
+NM_025474_Mrps14 chr1 162082365 162131317 + --- --- --- --- --- --- ---
+NM_025474_Mrps14 chr1 162082365 162131317 + --- --- --- --- --- --- ---
+NM_025505_Blzf1 chr1 166219931 166237615 - --- --- --- --- --- --- ---
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+NM_025505_Blzf1 chr1 166219931 166237615 - --- --- --- --- --- --- ---
+NM_025557_Pcp4l1 chr1 173103394 173126370 - --- --- --- --- --- --- ---
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+NM_025557_Pcp4l1 chr1 173103394 173126370 - --- --- --- --- --- --- ---
+NM_025557_Pcp4l1 chr1 173103394 173126370 - --- --- --- --- --- --- ---
+NM_025569_Mgst3 chr1 169302037 169323952 - --- --- --- --- --- --- ---
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+NM_025569_Mgst3 chr1 169302037 169323952 - --- --- --- --- --- --- ---
+NM_025569_Mgst3 chr1 169302037 169323952 - --- --- --- --- --- --- ---
+NM_025596_Prelid1 chr1 63410974 63469460 - --- --- --- --- --- --- ---
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+NM_025596_Prelid1 chr1 63410974 63469460 - --- --- --- --- --- --- ---
+NM_025596_Prelid1 chr1 63410974 63469460 - --- --- --- --- --- --- ---
+NM_025597_Ndufb3 chr1 58631453 58653239 + --- --- --- --- --- --- ---
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+NM_025597_Ndufb3 chr1 58631453 58653239 + --- --- --- --- --- --- ---
+NM_025677_Tsen15 chr1 154217920 154233812 - --- --- --- --- --- --- ---
+NM_025677_Tsen15 chr1 154217920 154233812 - --- --- --- --- --- --- ---
+NM_025677_Tsen15 chr1 154217920 154233812 - --- --- --- --- --- --- ---
+NM_025677_Tsen15 chr1 154217920 154233812 - --- --- --- --- --- --- ---
+NM_025683_Rpe chr1 66747223 66839854 + --- --- --- --- --- --- ---
+NM_025683_Rpe chr1 66747223 66839854 + --- --- --- --- --- --- ---
+NM_025683_Rpe chr1 66747223 66839854 + --- --- --- --- --- --- ---
+NM_025683_Rpe chr1 66747223 66839854 + --- --- --- --- --- --- ---
+NM_025746_4933415F23Rik chr1 23107346 23263222 - --- --- --- --- --- --- ---
+NM_025746_4933415F23Rik chr1 23107346 23263222 - --- --- --- --- --- --- ---
+NM_025746_4933415F23Rik chr1 23107346 23263222 - --- --- --- --- --- --- ---
+NM_025746_4933415F23Rik chr1 23107346 23263222 - --- --- --- --- --- --- ---
+NM_025773_Ube2w chr1 16530881 16609419 - --- --- --- --- --- --- ---
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+NM_025773_Ube2w chr1 16530881 16609419 - --- --- --- --- --- --- ---
+NM_025773_Ube2w chr1 16530881 16609419 - --- --- --- --- --- --- ---
+NM_025784_Bcs1l chr1 74634010 74639375 + --- --- --- --- --- --- ---
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+NM_025819_1200016B10Rik chr1 153214763 153304502 - --- --- --- --- --- --- ---
+NM_025819_1200016B10Rik chr1 153214763 153304502 - --- --- --- --- --- --- ---
+NM_025819_1200016B10Rik chr1 153214763 153304502 - --- --- --- --- --- --- ---
+NM_025819_1200016B10Rik chr1 153214763 153304502 - --- --- --- --- --- --- ---
+NM_025864_Tmem206 chr1 193149566 193176819 + --- --- --- --- --- --- ---
+NM_025864_Tmem206 chr1 193149566 193176819 + --- --- --- --- --- --- ---
+NM_025864_Tmem206 chr1 193149566 193176819 + --- --- --- --- --- --- ---
+NM_025864_Tmem206 chr1 193149566 193176819 + --- --- --- --- --- --- ---
+NM_025867_Serpinb11 chr1 109246610 109277052 + --- --- --- --- --- --- ---
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+NM_025920_Thap4 chr1 95602021 95651542 - --- --- --- --- --- --- ---
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+NM_025964_Fam119a chr1 64653048 64670990 - --- --- --- --- --- --- ---
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+NM_025964_Fam119a chr1 64653048 64670990 - --- --- --- --- --- --- ---
+NM_025964_Fam119a chr1 64653048 64670990 - --- --- --- --- --- --- ---
+NM_026024_Ube2t chr1 136857731 136870739 + chr1 136956468 136956598 85729 98737 U NO
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+NM_026024_Ube2t chr1 136857731 136870739 + --- --- --- --- --- --- ---
+NM_026041_Rrp15 chr1 188544857 188573732 - --- --- --- --- --- --- ---
+NM_026041_Rrp15 chr1 188544857 188573732 - --- --- --- --- --- --- ---
+NM_026041_Rrp15 chr1 188544857 188573732 - --- --- --- --- --- --- ---
+NM_026041_Rrp15 chr1 188544857 188573732 - --- --- --- --- --- --- ---
+NM_026078_Pigc chr1 163860747 163957217 + chr1 163827897 163828062 32685 32685 D NO
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+NM_026078_Pigc chr1 163860747 163957217 + --- --- --- --- --- --- ---
+NM_026078_Pigc chr1 163860747 163957217 + --- --- --- --- --- --- ---
+NM_026123_Unc50 chr1 37486671 37504876 + --- --- --- --- --- --- ---
+NM_026123_Unc50 chr1 37486671 37504876 + --- --- --- --- --- --- ---
+NM_026123_Unc50 chr1 37486671 37504876 + --- --- --- --- --- --- ---
+NM_026123_Unc50 chr1 37486671 37504876 + --- --- --- --- --- --- ---
+NM_026171_Nvl chr1 183008557 183074318 - --- --- --- --- --- --- ---
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+NM_026187_Ankzf1 chr1 75188977 75192143 + --- --- --- --- --- --- ---
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+NM_026187_Ankzf1 chr1 75188977 75192143 + --- --- --- --- --- --- ---
+NM_026187_Ankzf1 chr1 75192524 75195962 + --- --- --- --- --- --- ---
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+NM_026195_Atic chr1 71584010 71626205 + --- --- --- --- --- --- ---
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+NM_026234_Pigm chr1 174306609 174314210 + chr1 174376470 174376659 62260 69861 U NO
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+NM_026234_Pigm chr1 174306609 174314210 + --- --- --- --- --- --- ---
+NM_026234_Pigm chr1 174306609 174314210 + --- --- --- --- --- --- ---
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+NM_026241_Ankrd39 chr1 36594353 36604077 - --- --- --- --- --- --- ---
+NM_026250_Zh2c2 chr1 99658035 99706130 + --- --- --- --- --- --- ---
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+NM_026367_Gpatch2 chr1 189010707 189180483 + --- --- --- --- --- --- ---
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+NM_026375_Ahctf1 chr1 181675025 181733948 - --- --- --- --- --- --- ---
+NM_026380_Rgs8 chr1 155468581 155563679 + --- --- --- --- --- --- ---
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+NM_026390_Ubxn4 chr1 130140557 130175951 + --- --- --- --- --- --- ---
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+NM_026430_Uxs1 chr1 43804890 43884625 - --- --- --- --- --- --- ---
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+NM_026454_Ube2f chr1 93146888 93187187 + --- --- --- --- --- --- ---
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+NM_026456_Tceb1 chr1 16603307 16655630 - --- --- --- --- --- --- ---
+NM_026472_Mki67ip chr1 120218436 120230401 + --- --- --- --- --- --- ---
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+NM_026493_Cspp1 chr1 10028093 10126849 + --- --- --- --- --- --- ---
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+NM_026719_Lmbrd1 chr1 24593456 24847969 + chr1 24609562 24609623 0 16106 . YES
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+NM_026796_Smyd2 chr1 191704373 191746222 - --- --- --- --- --- --- ---
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+NM_026823_Arl8a chr1 137043216 137053347 + chr1 136956468 136956598 86618 86618 D NO
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+NM_026977_1810031K17Rik chr1 75131500 75139270 - --- --- --- --- --- --- ---
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+NM_027300_Spata3 chr1 87913403 87926533 + --- --- --- --- --- --- ---
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+NM_027351_Ppil3 chr1 58486110 58502330 - --- --- --- --- --- --- ---
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+NM_027407_Ica1l chr1 60039354 60099956 - --- --- --- --- --- --- ---
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+NM_027415_Tmem70 chr1 16610621 16668358 + --- --- --- --- --- --- ---
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+NM_027534_Kdsr chr1 108617007 108656357 - chr1 108747519 108747791 91162 91162 D NO
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+NM_027534_Kdsr chr1 108617007 108656357 - --- --- --- --- --- --- ---
+NM_027548_Serpinb7 chr1 109296172 109349266 + --- --- --- --- --- --- ---
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+NM_027548_Serpinb7 chr1 109296172 109349266 + --- --- --- --- --- --- ---
+NM_027551_Klhl30 chr1 93244259 93259068 + --- --- --- --- --- --- ---
+NM_027551_Klhl30 chr1 93244259 93259068 + --- --- --- --- --- --- ---
+NM_027551_Klhl30 chr1 93244259 93259068 + --- --- --- --- --- --- ---
+NM_027551_Klhl30 chr1 93244259 93259068 + --- --- --- --- --- --- ---
+NM_027637_4931428L18Rik chr1 31197921 31279501 - --- --- --- --- --- --- ---
+NM_027637_4931428L18Rik chr1 31197921 31279501 - --- --- --- --- --- --- ---
+NM_027637_4931428L18Rik chr1 31197921 31279501 - --- --- --- --- --- --- ---
+NM_027637_4931428L18Rik chr1 31197921 31279501 - --- --- --- --- --- --- ---
+NM_027661_Hsfy2 chr1 56668158 56822175 - --- --- --- --- --- --- ---
+NM_027661_Hsfy2 chr1 56668158 56822175 - --- --- --- --- --- --- ---
+NM_027661_Hsfy2 chr1 56668158 56822175 - --- --- --- --- --- --- ---
+NM_027661_Hsfy2 chr1 56668158 56822175 - --- --- --- --- --- --- ---
+NM_027677_Gpr39 chr1 127573518 127795359 + --- --- --- --- --- --- ---
+NM_027677_Gpr39 chr1 127573518 127795359 + --- --- --- --- --- --- ---
+NM_027677_Gpr39 chr1 127573518 127795359 + --- --- --- --- --- --- ---
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+NM_027678_Zranb3 chr1 129846941 130025531 - --- --- --- --- --- --- ---
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+NM_027725_Wdr69 chr1 83156310 83207145 + --- --- --- --- --- --- ---
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+NM_027884_Tns1 chr1 73956820 74144891 - --- --- --- --- --- --- ---
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+NM_027884_Tns1 chr1 73956820 74144891 - --- --- --- --- --- --- ---
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+NM_027886_Stk11ip chr1 75518100 75533910 + chr1 75481920 75482054 36046 36046 D NO
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+NM_027921_Slc16a14 chr1 84902046 84931841 - --- --- --- --- --- --- ---
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+NM_028333_Angptl1 chr1 158769061 158791209 + chr1 158835251 158835391 44042 66190 U NO
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+NM_028696_Obfc2a chr1 51417024 51550602 - --- --- --- --- --- --- ---
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+NM_028713_Rftn2 chr1 55227030 55283748 - chr1 55283572 55283675 0 73 . YES
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+NM_028848_Spata17 chr1 188868366 189039831 - --- --- --- --- --- --- ---
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+NM_033563_Klf7 chr1 64049920 64169179 - --- --- --- --- --- --- ---
+NM_033563_Klf7 chr1 64049920 64169179 - --- --- --- --- --- --- ---
+NM_033570_Cnnm4 chr1 36528452 36565609 + --- --- --- --- --- --- ---
+NM_033570_Cnnm4 chr1 36528452 36565609 + --- --- --- --- --- --- ---
+NM_033570_Cnnm4 chr1 36528452 36565609 + --- --- --- --- --- --- ---
+NM_033570_Cnnm4 chr1 36528452 36565609 + --- --- --- --- --- --- ---
+NM_033608_Igsf9 chr1 174411686 174429005 + chr1 174376470 174376659 35027 35027 D NO
+NM_033608_Igsf9 chr1 174411686 174429005 + --- --- --- --- --- --- ---
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+NM_033608_Igsf9 chr1 174411686 174429005 + --- --- --- --- --- --- ---
+NM_033652_Lmx1a chr1 169579767 169778872 + --- --- --- --- --- --- ---
+NM_033652_Lmx1a chr1 169579767 169778872 + --- --- --- --- --- --- ---
+NM_033652_Lmx1a chr1 169579767 169778872 + --- --- --- --- --- --- ---
+NM_033652_Lmx1a chr1 169579767 169778872 + --- --- --- --- --- --- ---
+NM_053015_Mlph chr1 92811657 92847814 + --- --- --- --- --- --- ---
+NM_053015_Mlph chr1 92811657 92847814 + --- --- --- --- --- --- ---
+NM_053015_Mlph chr1 92811657 92847814 + --- --- --- --- --- --- ---
+NM_053015_Mlph chr1 92811657 92847814 + --- --- --- --- --- --- ---
+NM_053095_Il24 chr1 132778072 132784021 - --- --- --- --- --- --- ---
+NM_053095_Il24 chr1 132778072 132784021 - --- --- --- --- --- --- ---
+NM_053095_Il24 chr1 132778072 132784021 - --- --- --- --- --- --- ---
+NM_053095_Il24 chr1 132778072 132784021 - --- --- --- --- --- --- ---
+NM_053106_Lmod1 chr1 137221395 137264642 + --- --- --- --- --- --- ---
+NM_053106_Lmod1 chr1 137221395 137264642 + --- --- --- --- --- --- ---
+NM_053106_Lmod1 chr1 137221395 137264642 + --- --- --- --- --- --- ---
+NM_053106_Lmod1 chr1 137221395 137264642 + --- --- --- --- --- --- ---
+NM_053107_Gpr45 chr1 43009719 43092301 + --- --- --- --- --- --- ---
+NM_053107_Gpr45 chr1 43009719 43092301 + --- --- --- --- --- --- ---
+NM_053107_Gpr45 chr1 43009719 43092301 + --- --- --- --- --- --- ---
+NM_053107_Gpr45 chr1 43009719 43092301 + --- --- --- --- --- --- ---
+NM_053191_Pi15 chr1 17591992 17621000 + --- --- --- --- --- --- ---
+NM_053191_Pi15 chr1 17591992 17621000 + --- --- --- --- --- --- ---
+NM_053191_Pi15 chr1 17591992 17621000 + --- --- --- --- --- --- ---
+NM_053191_Pi15 chr1 17591992 17621000 + --- --- --- --- --- --- ---
+NM_053199_Cadm3 chr1 175264723 175362523 - --- --- --- --- --- --- ---
+NM_053199_Cadm3 chr1 175264723 175362523 - --- --- --- --- --- --- ---
+NM_053199_Cadm3 chr1 175264723 175362523 - --- --- --- --- --- --- ---
+NM_053199_Cadm3 chr1 175264723 175362523 - --- --- --- --- --- --- ---
+NM_053257_Rpl31 chr1 39421000 39429094 + chr1 39492140 39492513 63046 71140 U NO
+NM_053257_Rpl31 chr1 39421000 39429094 + --- --- --- --- --- --- ---
+NM_053257_Rpl31 chr1 39421000 39429094 + --- --- --- --- --- --- ---
+NM_053257_Rpl31 chr1 39421000 39429094 + --- --- --- --- --- --- ---
+NM_053270_Rims1 chr1 22275987 22813178 - --- --- --- --- --- --- ---
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+NM_053270_Rims1 chr1 22275987 22813178 - --- --- --- --- --- --- ---
+NM_053270_Rims1 chr1 22275987 22813178 - --- --- --- --- --- --- ---
+NM_054076_Optc chr1 135787973 135805299 - chr1 135851853 135852218 46554 46554 D NO
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+NM_054076_Optc chr1 135787973 135805299 - --- --- --- --- --- --- ---
+NM_054076_Optc chr1 135787973 135805299 - --- --- --- --- --- --- ---
+NM_054077_Prelp chr1 135806855 135865173 - chr1 135851853 135852218 0 12955 . YES
+NM_054077_Prelp chr1 135806855 135865173 - --- --- --- --- --- --- ---
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+NM_054077_Prelp chr1 135806855 135865173 - --- --- --- --- --- --- ---
+NM_054087_Slc19a2 chr1 166178694 166196022 + --- --- --- --- --- --- ---
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+NM_054087_Slc19a2 chr1 166178694 166196022 + --- --- --- --- --- --- ---
+NM_054087_Slc19a2 chr1 166178694 166196022 + --- --- --- --- --- --- ---
+NM_054102_Ivns1abp chr1 153196503 153212127 + --- --- --- --- --- --- ---
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+NM_054102_Ivns1abp chr1 153196503 153212127 + --- --- --- --- --- --- ---
+NM_054102_Ivns1abp chr1 153196503 153212127 + --- --- --- --- --- --- ---
+NM_080419_Igsf8 chr1 174191772 174249967 + --- --- --- --- --- --- ---
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+NM_080419_Igsf8 chr1 174191772 174249967 + --- --- --- --- --- --- ---
+NM_080844_Serpinc1 chr1 162908738 162946004 + --- --- --- --- --- --- ---
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+NM_080844_Serpinc1 chr1 162908738 162946004 + --- --- --- --- --- --- ---
+NM_080850_Pask chr1 95205357 95240039 - chr1 95186508 95186637 18720 53402 U NO
+NM_080850_Pask chr1 95205357 95240039 - --- --- --- --- --- --- ---
+NM_080850_Pask chr1 95205357 95240039 - --- --- --- --- --- --- ---
+NM_080850_Pask chr1 95205357 95240039 - --- --- --- --- --- --- ---
+NM_130456_Nphs2 chr1 158233397 158258162 + --- --- --- --- --- --- ---
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+NM_130456_Nphs2 chr1 158233397 158258162 + --- --- --- --- --- --- ---
+NM_130456_Nphs2 chr1 158233397 158258162 + --- --- --- --- --- --- ---
+NM_130890_Capn8 chr1 184489366 184629001 + --- --- --- --- --- --- ---
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+NM_130890_Capn8 chr1 184489366 184629001 + --- --- --- --- --- --- ---
+NM_130890_Capn8 chr1 184489366 184629001 + --- --- --- --- --- --- ---
+NM_133193_Il1rl2 chr1 40381454 40447345 + chr1 40325917 40326123 55331 55331 D NO
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+NM_133193_Il1rl2 chr1 40381454 40447345 + --- --- --- --- --- --- ---
+NM_133220_Sgk3 chr1 9787936 9890911 + --- --- --- --- --- --- ---
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+NM_133225_Acbd3 chr1 182654006 182684317 + --- --- --- --- --- --- ---
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+NM_133235_Khdrbs2 chr1 32113056 32771277 + --- --- --- --- --- --- ---
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+NM_133239_Crb1 chr1 141093643 141296750 - --- --- --- --- --- --- ---
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+NM_133239_Crb1 chr1 141093643 141296750 - --- --- --- --- --- --- ---
+NM_133252_Tram2 chr1 20984161 21069306 - --- --- --- --- --- --- ---
+NM_133252_Tram2 chr1 20984161 21069306 - --- --- --- --- --- --- ---
+NM_133252_Tram2 chr1 20984161 21069306 - --- --- --- --- --- --- ---
+NM_133252_Tram2 chr1 20984161 21069306 - --- --- --- --- --- --- ---
+NM_133358_Zfp617 chr1 87909957 87912999 - --- --- --- --- --- --- ---
+NM_133358_Zfp617 chr1 87909957 87912999 - --- --- --- --- --- --- ---
+NM_133358_Zfp617 chr1 87909957 87912999 - --- --- --- --- --- --- ---
+NM_133358_Zfp617 chr1 87909957 87912999 - --- --- --- --- --- --- ---
+NM_133664_Lad1 chr1 137715163 137730085 + --- --- --- --- --- --- ---
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+NM_133664_Lad1 chr1 137715163 137730085 + --- --- --- --- --- --- ---
+NM_133684_Mosc2 chr1 186636947 186687141 - --- --- --- --- --- --- ---
+NM_133684_Mosc2 chr1 186636947 186687141 - --- --- --- --- --- --- ---
+NM_133684_Mosc2 chr1 186636947 186687141 - --- --- --- --- --- --- ---
+NM_133684_Mosc2 chr1 186636947 186687141 - --- --- --- --- --- --- ---
+NM_133705_Pycr2 chr1 182834431 182850616 + --- --- --- --- --- --- ---
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+NM_133728_Asnsd1 chr1 53382361 53409576 - --- --- --- --- --- --- ---
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+NM_133748_Insig2 chr1 123200933 123229157 - --- --- --- --- --- --- ---
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+NM_133780_Tpr chr1 152239968 152298193 + --- --- --- --- --- --- ---
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+NM_133781_Cab39 chr1 87687678 87748148 + --- --- --- --- --- --- ---
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+NM_133781_Cab39 chr1 87687678 87748148 + --- --- --- --- --- --- ---
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+NM_133805_Cops8 chr1 92499556 92564446 + --- --- --- --- --- --- ---
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+NM_133806_Uap1 chr1 172007106 172105098 - --- --- --- --- --- --- ---
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+NM_133808_Hdlbp chr1 95302520 95375513 - --- --- --- --- --- --- ---
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+NM_133809_Kmo chr1 177550532 177592237 + --- --- --- --- --- --- ---
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+NM_133810_Stk17b chr1 53812356 53857070 - --- --- --- --- --- --- ---
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+NM_133828_Creb1 chr1 64579391 64645546 + --- --- --- --- --- --- ---
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+NM_133828_Creb1 chr1 64646684 64649524 + --- --- --- --- --- --- ---
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+NM_144558_Bivm chr1 44175822 44201615 + chr1 44195449 44195639 0 19627 . YES
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+NM_144791_Tor1aip1 chr1 157851734 157889804 - --- --- --- --- --- --- ---
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+NM_144794_Tmem63a chr1 182872430 182919700 + --- --- --- --- --- --- ---
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+NM_144814_Rcor3 chr1 193910981 193962565 - --- --- --- --- --- --- ---
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+NM_144814_Rcor3 chr1 193910981 193962565 - --- --- --- --- --- --- ---
+NM_144814_Rcor3 chr1 193910981 193962565 - --- --- --- --- --- --- ---
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+NM_178884_Obsl1 chr1 75482401 75503218 - --- --- --- --- --- --- ---
+NM_181405_Rnpepl1 chr1 94807467 94817954 + --- --- --- --- --- --- ---
+NM_181405_Rnpepl1 chr1 94807467 94817954 + --- --- --- --- --- --- ---
+NM_181405_Rnpepl1 chr1 94807467 94817954 + --- --- --- --- --- --- ---
+NM_181405_Rnpepl1 chr1 94807467 94817954 + --- --- --- --- --- --- ---
+NM_181546_Syt14 chr1 194713536 194861959 - chr1 194957396 194957723 95437 95437 D NO
+NM_181546_Syt14 chr1 194713536 194861959 - --- --- --- --- --- --- ---
+NM_181546_Syt14 chr1 194713536 194861959 - --- --- --- --- --- --- ---
+NM_181546_Syt14 chr1 194713536 194861959 - --- --- --- --- --- --- ---
+NM_181750_R3hdm1 chr1 129999892 130134312 + --- --- --- --- --- --- ---
+NM_181750_R3hdm1 chr1 129999892 130134312 + --- --- --- --- --- --- ---
+NM_181750_R3hdm1 chr1 129999892 130134312 + --- --- --- --- --- --- ---
+NM_181750_R3hdm1 chr1 129999892 130134312 + --- --- --- --- --- --- ---
+NM_181796_Gstp2 chr1 193897651 193905509 - --- --- --- --- --- --- ---
+NM_181796_Gstp2 chr1 193897651 193905509 - --- --- --- --- --- --- ---
+NM_181796_Gstp2 chr1 193897651 193905509 - --- --- --- --- --- --- ---
+NM_181796_Gstp2 chr1 193897651 193905509 - --- --- --- --- --- --- ---
+NM_182716_Nfasc chr1 134445291 134638354 - --- --- --- --- --- --- ---
+NM_182716_Nfasc chr1 134445291 134638354 - --- --- --- --- --- --- ---
+NM_182716_Nfasc chr1 134445291 134638354 - --- --- --- --- --- --- ---
+NM_182716_Nfasc chr1 134445291 134638354 - --- --- --- --- --- --- ---
+NM_182930_Plekha6 chr1 135077806 135200008 + --- --- --- --- --- --- ---
+NM_182930_Plekha6 chr1 135077806 135200008 + --- --- --- --- --- --- ---
+NM_182930_Plekha6 chr1 135077806 135200008 + --- --- --- --- --- --- ---
+NM_182930_Plekha6 chr1 135077806 135200008 + --- --- --- --- --- --- ---
+NM_183019_Arhgef4 chr1 34788954 34873560 + --- --- --- --- --- --- ---
+NM_183019_Arhgef4 chr1 34788954 34873560 + --- --- --- --- --- --- ---
+NM_183019_Arhgef4 chr1 34788954 34873560 + --- --- --- --- --- --- ---
+NM_183019_Arhgef4 chr1 34788954 34873560 + --- --- --- --- --- --- ---
+NM_183022_Accn4 chr1 75447063 75470207 + chr1 75481920 75482054 11713 34857 U NO
+NM_183022_Accn4 chr1 75447063 75470207 + --- --- --- --- --- --- ---
+NM_183022_Accn4 chr1 75447063 75470207 + --- --- --- --- --- --- ---
+NM_183022_Accn4 chr1 75447063 75470207 + --- --- --- --- --- --- ---
+NM_183027_Ap1s3 chr1 79591820 79668545 - --- --- --- --- --- --- ---
+NM_183027_Ap1s3 chr1 79591820 79668545 - --- --- --- --- --- --- ---
+NM_183027_Ap1s3 chr1 79591820 79668545 - --- --- --- --- --- --- ---
+NM_183027_Ap1s3 chr1 79591820 79668545 - --- --- --- --- --- --- ---
+NM_183028_Pcmtd1 chr1 7079053 7163709 + --- --- --- --- --- --- ---
+NM_183028_Pcmtd1 chr1 7079053 7163709 + --- --- --- --- --- --- ---
+NM_183028_Pcmtd1 chr1 7079053 7163709 + --- --- --- --- --- --- ---
+NM_183028_Pcmtd1 chr1 7079053 7163709 + --- --- --- --- --- --- ---
+NM_183124_Defb41 chr1 18241071 18350659 - --- --- --- --- --- --- ---
+NM_183124_Defb41 chr1 18241071 18350659 - --- --- --- --- --- --- ---
+NM_183124_Defb41 chr1 18241071 18350659 - --- --- --- --- --- --- ---
+NM_183124_Defb41 chr1 18241071 18350659 - --- --- --- --- --- --- ---
+NM_183355_Pbx1 chr1 170049495 170512777 - --- --- --- --- --- --- ---
+NM_183355_Pbx1 chr1 170049495 170512777 - --- --- --- --- --- --- ---
+NM_183355_Pbx1 chr1 170049495 170512777 - --- --- --- --- --- --- ---
+NM_183355_Pbx1 chr1 170049495 170512777 - --- --- --- --- --- --- ---
+NM_183391_Tnfsf18 chr1 163373523 163524094 + --- --- --- --- --- --- ---
+NM_183391_Tnfsf18 chr1 163373523 163524094 + --- --- --- --- --- --- ---
+NM_183391_Tnfsf18 chr1 163373523 163524094 + --- --- --- --- --- --- ---
+NM_183391_Tnfsf18 chr1 163373523 163524094 + --- --- --- --- --- --- ---
+NM_194333_Slc23a3 chr1 75120731 75130464 - --- --- --- --- --- --- ---
+NM_194333_Slc23a3 chr1 75120731 75130464 - --- --- --- --- --- --- ---
+NM_194333_Slc23a3 chr1 75120731 75130464 - --- --- --- --- --- --- ---
+NM_194333_Slc23a3 chr1 75120731 75130464 - --- --- --- --- --- --- ---
+NM_198006_6330578E17Rik chr1 37473934 37474944 - --- --- --- --- --- --- ---
+NM_198006_6330578E17Rik chr1 37473934 37474944 - --- --- --- --- --- --- ---
+NM_198006_6330578E17Rik chr1 37473934 37474944 - --- --- --- --- --- --- ---
+NM_198006_6330578E17Rik chr1 37473934 37474944 - --- --- --- --- --- --- ---
+NM_198006_6330578E17Rik chr1 37477057 37486928 - --- --- --- --- --- --- ---
+NM_198006_6330578E17Rik chr1 37477057 37486928 - --- --- --- --- --- --- ---
+NM_198006_6330578E17Rik chr1 37477057 37486928 - --- --- --- --- --- --- ---
+NM_198006_6330578E17Rik chr1 37477057 37486928 - --- --- --- --- --- --- ---
+NM_198028_Serpinb10 chr1 109425580 109445838 + --- --- --- --- --- --- ---
+NM_198028_Serpinb10 chr1 109425580 109445838 + --- --- --- --- --- --- ---
+NM_198028_Serpinb10 chr1 109425580 109445838 + --- --- --- --- --- --- ---
+NM_198028_Serpinb10 chr1 109425580 109445838 + --- --- --- --- --- --- ---
+NM_198127_Abi2 chr1 60466022 60537998 + --- --- --- --- --- --- ---
+NM_198127_Abi2 chr1 60466022 60537998 + --- --- --- --- --- --- ---
+NM_198127_Abi2 chr1 60466022 60537998 + --- --- --- --- --- --- ---
+NM_198127_Abi2 chr1 60466022 60537998 + --- --- --- --- --- --- ---
+NM_198247_Sertad4 chr1 194670313 194693726 - chr1 194645118 194645475 24838 48251 U NO
+NM_198247_Sertad4 chr1 194670313 194693726 - --- --- --- --- --- --- ---
+NM_198247_Sertad4 chr1 194670313 194693726 - --- --- --- --- --- --- ---
+NM_198247_Sertad4 chr1 194670313 194693726 - --- --- --- --- --- --- ---
+NM_198303_Eif5b chr1 38054627 38112414 + --- --- --- --- --- --- ---
+NM_198303_Eif5b chr1 38054627 38112414 + --- --- --- --- --- --- ---
+NM_198303_Eif5b chr1 38054627 38112414 + --- --- --- --- --- --- ---
+NM_198303_Eif5b chr1 38054627 38112414 + --- --- --- --- --- --- ---
+NM_198652_6430706D22Rik chr1 90158880 90174174 - --- --- --- --- --- --- ---
+NM_198652_6430706D22Rik chr1 90158880 90174174 - --- --- --- --- --- --- ---
+NM_198652_6430706D22Rik chr1 90158880 90174174 - --- --- --- --- --- --- ---
+NM_198652_6430706D22Rik chr1 90158880 90174174 - --- --- --- --- --- --- ---
+NM_198653_Iars2 chr1 187109458 187153280 - --- --- --- --- --- --- ---
+NM_198653_Iars2 chr1 187109458 187153280 - --- --- --- --- --- --- ---
+NM_198653_Iars2 chr1 187109458 187153280 - --- --- --- --- --- --- ---
+NM_198653_Iars2 chr1 187109458 187153280 - --- --- --- --- --- --- ---
+NM_198654_Nsl1 chr1 192886918 192919389 + --- --- --- --- --- --- ---
+NM_198654_Nsl1 chr1 192886918 192919389 + --- --- --- --- --- --- ---
+NM_198654_Nsl1 chr1 192886918 192919389 + --- --- --- --- --- --- ---
+NM_198654_Nsl1 chr1 192886918 192919389 + --- --- --- --- --- --- ---
+NM_198680_Serpinb3b chr1 109033488 109059720 - --- --- --- --- --- --- ---
+NM_198680_Serpinb3b chr1 109033488 109059720 - --- --- --- --- --- --- ---
+NM_198680_Serpinb3b chr1 109033488 109059720 - --- --- --- --- --- --- ---
+NM_198680_Serpinb3b chr1 109033488 109059720 - --- --- --- --- --- --- ---
+NM_198899_Ugcgl1 chr1 36196873 36301555 - --- --- --- --- --- --- ---
+NM_198899_Ugcgl1 chr1 36196873 36301555 - --- --- --- --- --- --- ---
+NM_198899_Ugcgl1 chr1 36196873 36301555 - --- --- --- --- --- --- ---
+NM_198899_Ugcgl1 chr1 36196873 36301555 - --- --- --- --- --- --- ---
+NM_198934_Pou2f1 chr1 167804181 167932753 - chr1 167906284 167906554 0 26199 . YES
+NM_198934_Pou2f1 chr1 167804181 167932753 - --- --- --- --- --- --- ---
+NM_198934_Pou2f1 chr1 167804181 167932753 - --- --- --- --- --- --- ---
+NM_198934_Pou2f1 chr1 167804181 167932753 - --- --- --- --- --- --- ---
+NM_199007_Sgol2 chr1 58026657 58085164 + --- --- --- --- --- --- ---
+NM_199007_Sgol2 chr1 58026657 58085164 + --- --- --- --- --- --- ---
+NM_199007_Sgol2 chr1 58026657 58085164 + --- --- --- --- --- --- ---
+NM_199007_Sgol2 chr1 58026657 58085164 + --- --- --- --- --- --- ---
+NM_199021_Dpp10 chr1 125044486 126749525 - --- --- --- --- --- --- ---
+NM_199021_Dpp10 chr1 125044486 126749525 - --- --- --- --- --- --- ---
+NM_199021_Dpp10 chr1 125044486 126749525 - --- --- --- --- --- --- ---
+NM_199021_Dpp10 chr1 125044486 126749525 - --- --- --- --- --- --- ---
+NM_201363_Serpinb3c chr1 109088051 109198931 - --- --- --- --- --- --- ---
+NM_201363_Serpinb3c chr1 109088051 109198931 - --- --- --- --- --- --- ---
+NM_201363_Serpinb3c chr1 109088051 109198931 - --- --- --- --- --- --- ---
+NM_201363_Serpinb3c chr1 109088051 109198931 - --- --- --- --- --- --- ---
+NM_201376_Serpinb3d chr1 108974770 108980057 - --- --- --- --- --- --- ---
+NM_201376_Serpinb3d chr1 108974770 108980057 - --- --- --- --- --- --- ---
+NM_201376_Serpinb3d chr1 108974770 108980057 - --- --- --- --- --- --- ---
+NM_201376_Serpinb3d chr1 108974770 108980057 - --- --- --- --- --- --- ---
+NM_201641_Ugt1a10 chr1 89922380 90115570 + chr1 89989553 89989714 0 67173 . YES
+NM_201641_Ugt1a10 chr1 89922380 90115570 + --- --- --- --- --- --- ---
+NM_201641_Ugt1a10 chr1 89922380 90115570 + --- --- --- --- --- --- ---
+NM_201641_Ugt1a10 chr1 89922380 90115570 + --- --- --- --- --- --- ---
+NM_206896_Olfr12 chr1 94516341 94538591 + --- --- --- --- --- --- ---
+NM_206896_Olfr12 chr1 94516341 94538591 + --- --- --- --- --- --- ---
+NM_206896_Olfr12 chr1 94516341 94538591 + --- --- --- --- --- --- ---
+NM_206896_Olfr12 chr1 94516341 94538591 + --- --- --- --- --- --- ---
+NM_207031_Ano7 chr1 95270385 95302271 + chr1 95186508 95186637 83748 83748 D NO
+NM_207031_Ano7 chr1 95270385 95302271 + --- --- --- --- --- --- ---
+NM_207031_Ano7 chr1 95270385 95302271 + --- --- --- --- --- --- ---
+NM_207031_Ano7 chr1 95270385 95302271 + --- --- --- --- --- --- ---
+NM_207137_Olfr417 chr1 176299050 176299979 + --- --- --- --- --- --- ---
+NM_207137_Olfr417 chr1 176299050 176299979 + --- --- --- --- --- --- ---
+NM_207137_Olfr417 chr1 176299050 176299979 + --- --- --- --- --- --- ---
+NM_207137_Olfr417 chr1 176299050 176299979 + --- --- --- --- --- --- ---
+NM_207137_Olfr417 chr1 176321202 176322113 + --- --- --- --- --- --- ---
+NM_207137_Olfr417 chr1 176321202 176322113 + --- --- --- --- --- --- ---
+NM_207137_Olfr417 chr1 176321202 176322113 + --- --- --- --- --- --- ---
+NM_207137_Olfr417 chr1 176321202 176322113 + --- --- --- --- --- --- ---
+NM_207158_Olfr427 chr1 176028781 176030538 + --- --- --- --- --- --- ---
+NM_207158_Olfr427 chr1 176028781 176030538 + --- --- --- --- --- --- ---
+NM_207158_Olfr427 chr1 176028781 176030538 + --- --- --- --- --- --- ---
+NM_207158_Olfr427 chr1 176028781 176030538 + --- --- --- --- --- --- ---
+NM_207225_Hdac4 chr1 93755950 94103099 - --- --- --- --- --- --- ---
+NM_207225_Hdac4 chr1 93755950 94103099 - --- --- --- --- --- --- ---
+NM_207225_Hdac4 chr1 93755950 94103099 - --- --- --- --- --- --- ---
+NM_207225_Hdac4 chr1 93755950 94103099 - --- --- --- --- --- --- ---
+NM_207228_Tsga10 chr1 37783457 37922148 - --- --- --- --- --- --- ---
+NM_207228_Tsga10 chr1 37783457 37922148 - --- --- --- --- --- --- ---
+NM_207228_Tsga10 chr1 37783457 37922148 - --- --- --- --- --- --- ---
+NM_207228_Tsga10 chr1 37783457 37922148 - --- --- --- --- --- --- ---
+NM_207233_C1ql2 chr1 122196386 122239751 + --- --- --- --- --- --- ---
+NM_207233_C1ql2 chr1 122196386 122239751 + --- --- --- --- --- --- ---
+NM_207233_C1ql2 chr1 122196386 122239751 + --- --- --- --- --- --- ---
+NM_207233_C1ql2 chr1 122196386 122239751 + --- --- --- --- --- --- ---
+NM_207281_4832428D23Rik chr1 44260915 44515719 - --- --- --- --- --- --- ---
+NM_207281_4832428D23Rik chr1 44260915 44515719 - --- --- --- --- --- --- ---
+NM_207281_4832428D23Rik chr1 44260915 44515719 - --- --- --- --- --- --- ---
+NM_207281_4832428D23Rik chr1 44260915 44515719 - --- --- --- --- --- --- ---
+NM_207583_Fam5b chr1 160175402 160286644 - --- --- --- --- --- --- ---
+NM_207583_Fam5b chr1 160175402 160286644 - --- --- --- --- --- --- ---
+NM_207583_Fam5b chr1 160175402 160286644 - --- --- --- --- --- --- ---
+NM_207583_Fam5b chr1 160175402 160286644 - --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58768296 58813658 + --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58768296 58813658 + --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58768296 58813658 + --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58768296 58813658 + --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58813703 58815725 + --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58813703 58815725 + --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58813703 58815725 + --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58813703 58815725 + --- --- --- --- --- --- ---
+NM_213616_Atp2b4 chr1 135602265 135697538 - chr1 135582677 135582828 19437 114710 U NO
+NM_213616_Atp2b4 chr1 135602265 135697538 - --- --- --- --- --- --- ---
+NM_213616_Atp2b4 chr1 135602265 135697538 - --- --- --- --- --- --- ---
+NM_213616_Atp2b4 chr1 135602265 135697538 - --- --- --- --- --- --- ---
+NR_002840_Gas5 chr1 162964758 162968663 + --- --- --- --- --- --- ---
+NR_002840_Gas5 chr1 162964758 162968663 + --- --- --- --- --- --- ---
+NR_002840_Gas5 chr1 162964758 162968663 + --- --- --- --- --- --- ---
+NR_002840_Gas5 chr1 162964758 162968663 + --- --- --- --- --- --- ---
+NR_002858_EG241041 chr1 21268965 21306401 - --- --- --- --- --- --- ---
+NR_002858_EG241041 chr1 21268965 21306401 - --- --- --- --- --- --- ---
+NR_002858_EG241041 chr1 21268965 21306401 - --- --- --- --- --- --- ---
+NR_002858_EG241041 chr1 21268965 21306401 - --- --- --- --- --- --- ---
+NR_002870_Dnm3os chr1 164119785 164155671 + chr1 164215623 164215935 59952 95838 U NO
+NR_002870_Dnm3os chr1 164119785 164155671 + --- --- --- --- --- --- ---
+NR_002870_Dnm3os chr1 164119785 164155671 + --- --- --- --- --- --- ---
+NR_002870_Dnm3os chr1 164119785 164155671 + --- --- --- --- --- --- ---
+NR_003623_EG277333 chr1 182251970 182262902 - --- --- --- --- --- --- ---
+NR_003623_EG277333 chr1 182251970 182262902 - --- --- --- --- --- --- ---
+NR_003623_EG277333 chr1 182251970 182262902 - --- --- --- --- --- --- ---
+NR_003623_EG277333 chr1 182251970 182262902 - --- --- --- --- --- --- ---
+NR_026896_4931440L10Rik chr1 136437533 136449760 - --- --- --- --- --- --- ---
+NR_026896_4931440L10Rik chr1 136437533 136449760 - --- --- --- --- --- --- ---
+NR_026896_4931440L10Rik chr1 136437533 136449760 - --- --- --- --- --- --- ---
+NR_026896_4931440L10Rik chr1 136437533 136449760 - --- --- --- --- --- --- ---
diff -r 000000000000 -r 0abe6bac47a6 test-data/peaks_per_feature4.summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peaks_per_feature4.summary Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,957 @@
+#gene.id gene.chr gene.start gene.end gene.strand chr start end dist_closest dist_TSS direction in_the_gene
+AF064749_Col6a3 chr1 92566771 92800755 - --- --- --- --- --- --- ---
+AK015559_4930472D16Rik chr1 25020851 25021989 - --- --- --- --- --- --- ---
+AK030377_A330023F24Rik chr1 196781953 196826186 - --- --- --- --- --- --- ---
+AK080193_A530079E22Rik chr1 89401837 89403491 - --- --- --- --- --- --- ---
+AK082264_C230030N03Rik chr1 34735043 34781084 + --- --- --- --- --- --- ---
+BC006931_AI597479 chr1 43153807 43172843 + --- --- --- --- --- --- ---
+BC021773_Glb1l chr1 75193364 75207353 - --- --- --- --- --- --- ---
+BC023951_D1Ertd622e chr1 99540054 99558631 - --- --- --- --- --- --- ---
+BC028767_3110009E18Rik chr1 122017764 122114603 + --- --- --- --- --- --- ---
+BC031781_BC031781 chr1 182781250 182798240 + --- --- --- --- --- --- ---
+BC034187_BC035947 chr1 78493611 78497758 - --- --- --- --- --- --- ---
+BC043098_Fam168b chr1 34870072 34917183 - --- --- --- --- --- --- ---
+BC049091_D1Bwg0212e chr1 39592545 39603734 + chr1 39492140 39492513 100032 100032 D NO
+BC049713_Ankrd45 chr1 163072817 163099826 + --- --- --- --- --- --- ---
+BC050813_4921511C04Rik chr1 37157481 37244861 + --- --- --- --- --- --- ---
+BC051128_4921521F21Rik chr1 65059273 65079312 - --- --- --- --- --- --- ---
+BC052693_2810422O20Rik chr1 165924541 165927371 + --- --- --- --- --- --- ---
+BC052931_A630001G21Rik chr1 87601462 87674840 - --- --- --- --- --- --- ---
+BC053100_5730559C18Rik chr1 138110108 138130841 - --- --- --- --- --- --- ---
+BC054802_9630058J23Rik chr1 181476521 181558044 + --- --- --- --- --- --- ---
+BC055845_2810025M15Rik chr1 159342483 159350353 + chr1 159240736 159240866 101617 101617 D NO
+BC055955_A130010J15Rik chr1 194999663 195004015 + chr1 194957396 194957723 41940 41940 D NO
+BC057872_Rab3gap2 chr1 187028006 187110623 + --- --- --- --- --- --- ---
+BC058417_2610017I09Rik chr1 42648822 42751667 - --- --- --- --- --- --- ---
+BC059254_Phlpp chr1 108042052 108306367 + --- --- --- --- --- --- ---
+BC070435_Fam123c chr1 34620070 34671545 + --- --- --- --- --- --- ---
+BC070446_Fam135a chr1 24017617 24107170 - --- --- --- --- --- --- ---
+BC071241_9430016H08Rik chr1 57463192 57497936 + --- --- --- --- --- --- ---
+BC072639_2010300C02Rik chr1 37646877 37776659 - --- --- --- --- --- --- ---
+BC080290_5033414K04Rik chr1 84032539 84360735 - --- --- --- --- --- --- ---
+BC082310_9430031J16Rik chr1 81073525 81338329 + --- --- --- --- --- --- ---
+BC089525_2310007B03Rik chr1 95047933 95063386 - chr1 95186508 95186637 123122 123122 D NO
+BC089561_Cep350 chr1 157692096 157820375 - --- --- --- --- --- --- ---
+BC147491_A230074B11Rik chr1 37083441 37133840 + --- --- --- --- --- --- ---
+BC147657_9630028B13Rik chr1 187253234 187265698 - --- --- --- --- --- --- ---
+ENSMUST00000027997_Rgs5 chr1 171625108 171625913 + --- --- --- --- --- --- ---
+ENSMUST00000051203_1700001G17Rik chr1 33726669 33727551 + --- --- --- --- --- --- ---
+ENSMUST00000054333_A130050O07Rik chr1 139823828 139826840 + --- --- --- --- --- --- ---
+ENSMUST00000056879_C230029F24Rik chr1 49301475 49397265 + --- --- --- --- --- --- ---
+ENSMUST00000057543_A730013G03Rik chr1 194659323 194661397 - chr1 194645118 194645475 13848 15922 U NO
+ENSMUST00000062637_4930470H14Rik chr1 175156866 175201240 + --- --- --- --- --- --- ---
+ENSMUST00000070048_ENSMUSG00000056128 chr1 92571736 92576368 + --- --- --- --- --- --- ---
+ENSMUST00000070987_EG433384 chr1 183781705 183783320 - --- --- --- --- --- --- ---
+ENSMUST00000072395_Olfr1406 chr1 175113651 175120746 - --- --- --- --- --- --- ---
+ENSMUST00000094288_Wdr64 chr1 177654798 177798070 + --- --- --- --- --- --- ---
+ENSMUST00000094950_Pgap1 chr1 54529849 54614539 - chr1 54631692 54631815 17153 17153 D NO
+ENSMUST00000097776_Cnnm3 chr1 36567938 36585164 + --- --- --- --- --- --- ---
+EU429481_Igfn1 chr1 137825893 137890307 - --- --- --- --- --- --- ---
+FJ024495_Ildr2 chr1 168236882 168239692 - --- --- --- --- --- --- ---
+FJ210934_Unc80 chr1 66514856 66556109 + --- --- --- --- --- --- ---
+NM_001001565_Chpf chr1 75470923 75476437 - chr1 75481920 75482054 5483 5483 D NO
+NM_001001809_Olfr218 chr1 175130421 175134469 + --- --- --- --- --- --- ---
+NM_001001883_Hecw2 chr1 53867026 54252002 - --- --- --- --- --- --- ---
+NM_001003917_Atg9a chr1 75177439 75189181 - --- --- --- --- --- --- ---
+NM_001004173_Sgpp2 chr1 78306692 78416864 + --- --- --- --- --- --- ---
+NM_001005423_Mreg chr1 72170192 72258895 - --- --- --- --- --- --- ---
+NM_001005507_Smg7 chr1 154684125 154750410 - --- --- --- --- --- --- ---
+NM_001005508_Arhgap30 chr1 173319072 173340822 + --- --- --- --- --- --- ---
+NM_001005520_Olfr244 chr1 176032571 176067605 - --- --- --- --- --- --- ---
+NM_001008419_Aox3l1 chr1 58335180 58437083 + --- --- --- --- --- --- ---
+NM_001008426_EG433365 chr1 155721475 155724001 + --- --- --- --- --- --- ---
+NM_001008533_Adora1 chr1 136095799 136181661 - --- --- --- --- --- --- ---
+NM_001009940_Il19 chr1 132786042 132915234 - chr1 132950929 132951247 35695 35695 D NO
+NM_001011525_Olfr1415 chr1 94376258 94381054 - --- --- --- --- --- --- ---
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+NM_010933_Nppc chr1 88512597 88567147 - --- --- --- --- --- --- ---
+NM_011011_Oprk1 chr1 5578025 5596202 + --- --- --- --- --- --- ---
+NM_011063_Pea15a chr1 174126043 174136915 - --- --- --- --- --- --- ---
+NM_011066_Per2 chr1 93312559 93386413 - --- --- --- --- --- --- ---
+NM_011070_Pfdn2 chr1 173275115 173289384 + --- --- --- --- --- --- ---
+NM_011082_Pigr chr1 132723238 132748826 + --- --- --- --- --- --- ---
+NM_011086_Pikfyve chr1 65225807 65332228 + --- --- --- --- --- --- ---
+NM_011111_Serpinb2 chr1 109407675 109422169 + --- --- --- --- --- --- ---
+NM_011198_Ptgs2 chr1 151947054 152026155 + --- --- --- --- --- --- ---
+NM_011206_Ptpn18 chr1 34516613 34532568 + --- --- --- --- --- --- ---
+NM_011267_Rgs16 chr1 155574693 155592596 + --- --- --- --- --- --- ---
+NM_011273_Xpr1 chr1 157103002 157264554 - --- --- --- --- --- --- ---
+NM_011277_Rnf2 chr1 153305192 153359013 - --- --- --- --- --- --- ---
+NM_011283_Rp1 chr1 3989638 4469288 - --- --- --- --- --- --- ---
+NM_011318_Apcs chr1 174824092 174855560 - --- --- --- --- --- --- ---
+NM_011345_Sele chr1 165978323 165988607 + --- --- --- --- --- --- ---
+NM_011346_Sell chr1 165992132 166007817 + --- --- --- --- --- --- ---
+NM_011347_Selp chr1 166045416 166080154 + --- --- --- --- --- --- ---
+NM_011439_Sox13 chr1 135278853 135384763 - --- --- --- --- --- --- ---
+NM_011441_Sox17 chr1 4481009 4487839 - --- --- --- --- --- --- ---
+NM_011459_Serpinb8 chr1 109486542 109586251 + --- --- --- --- --- --- ---
+NM_011465_Spna1 chr1 176102906 176178561 + --- --- --- --- --- --- ---
+NM_011487_Stat4 chr1 52036485 52164030 + --- --- --- --- --- --- ---
+NM_011494_Stk16 chr1 75207414 75212181 + --- --- --- --- --- --- ---
+NM_011541_Tcea1 chr1 4847584 4889703 + --- --- --- --- --- --- ---
+NM_011590_Timm17a chr1 137197272 137210335 - --- --- --- --- --- --- ---
+NM_011633_Traf5 chr1 193821096 193916369 - --- --- --- --- --- --- ---
+NM_011650_Tsn chr1 120194658 120208016 - --- --- --- --- --- --- ---
+NM_011729_Ercc5 chr1 44204270 44256568 + chr1 44195449 44195639 8631 8631 D NO
+NM_011770_Ikzf2 chr1 69574124 69733875 - --- --- --- --- --- --- ---
+NM_011780_Adam23 chr1 63482194 63639230 + --- --- --- --- --- --- ---
+NM_011780_Adam23 chr1 63640970 63642850 + chr1 63664888 63665018 22038 23918 U NO
+NM_011785_Akt3 chr1 178940936 179188314 - --- --- --- --- --- --- ---
+NM_011794_Bpnt1 chr1 187156058 187181696 + --- --- --- --- --- --- ---
+NM_011796_Capn10 chr1 94830953 94844518 + --- --- --- --- --- --- ---
+NM_011800_Cdh20 chr1 106665116 106892058 + --- --- --- --- --- --- ---
+NM_011804_Creg1 chr1 167693878 167710825 + --- --- --- --- --- --- ---
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+NM_011882_Rnasel chr1 155596576 155619417 + --- --- --- --- --- --- ---
+NM_011931_Rfwd2 chr1 161159948 161307408 + --- --- --- --- --- --- ---
+NM_011935_Esrrg chr1 189432683 190062059 + --- --- --- --- --- --- ---
+NM_012009_Sh2d1b1 chr1 172162900 172220030 + --- --- --- --- --- --- ---
+NM_012012_Exo1 chr1 177810732 177841721 + --- --- --- --- --- --- ---
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+NM_013474_Apoa2 chr1 173151908 173156502 + --- --- --- --- --- --- ---
+NM_013489_Cd84 chr1 173769848 173820852 + --- --- --- --- --- --- ---
+NM_013499_Cr1l chr1 196924298 196957754 - chr1 197057796 197057843 100042 100042 D NO
+NM_013612_Slc11a1 chr1 74421758 74433050 + --- --- --- --- --- --- ---
+NM_013626_Pam chr1 99691711 100053468 - --- --- --- --- --- --- ---
+NM_013673_Sp100 chr1 84943347 87618694 + --- --- --- --- --- --- ---
+NM_013715_Cops5 chr1 10014683 10028315 - --- --- --- --- --- --- ---
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+NM_013750_Phlda3 chr1 137662671 137665710 + --- --- --- --- --- --- ---
+NM_013784_Pign chr1 107385512 107560244 - --- --- --- --- --- --- ---
+NM_013835_Trove2 chr1 145597816 145624178 - chr1 145591041 145591176 6640 33002 U NO
+NM_013862_Rabgap1l chr1 162149308 162739582 - --- --- --- --- --- --- ---
+NM_013919_Usp21 chr1 173212080 173218102 - --- --- --- --- --- --- ---
+NM_015750_Neu2 chr1 89348720 89494397 + --- --- --- --- --- --- ---
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+NM_015818_Hs6st1 chr1 36125255 36163289 + chr1 36106813 36107058 18197 18197 D NO
+NM_016696_Gpc1 chr1 94728253 94757346 + --- --- --- --- --- --- ---
+NM_016702_Agxt chr1 95031777 95041991 + --- --- --- --- --- --- ---
+NM_016716_Cul3 chr1 80261498 80323399 - --- --- --- --- --- --- ---
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+NM_016778_Bok chr1 95579016 95592340 + --- --- --- --- --- --- ---
+NM_016796_Vamp4 chr1 164500371 164532593 + --- --- --- --- --- --- ---
+NM_016805_Hnrnpu chr1 180251245 180298730 - --- --- --- --- --- --- ---
+NM_016846_Rgl1 chr1 154357421 154613475 - --- --- --- --- --- --- ---
+NM_016851_Irf6 chr1 194979326 194998230 + chr1 194957396 194957723 21603 21603 D NO
+NM_016894_Ramp1 chr1 93076419 93120251 + --- --- --- --- --- --- ---
+NM_016894_Ramp1 chr1 93120257 93121772 + --- --- --- --- --- --- ---
+NM_016916_Blcap chr1 46068602 46087314 - --- --- --- --- --- --- ---
+NM_016917_Slc40a1 chr1 45964925 45999090 - --- --- --- --- --- --- ---
+NM_016923_Ly96 chr1 16678152 16699618 + --- --- --- --- --- --- ---
+NM_016928_Tlr5 chr1 184884929 184903333 + --- --- --- --- --- --- ---
+NM_016960_Ccl20 chr1 83112527 83138624 + --- --- --- --- --- --- ---
+NM_017480_Icos chr1 61034747 61057162 + --- --- --- --- --- --- ---
+NM_018729_Cd244 chr1 173481630 173515439 + --- --- --- --- --- --- ---
+NM_018750_Rassf5 chr1 133072991 133144761 - chr1 133114860 133115015 0 29746 . YES
+NM_018775_Tbc1d8 chr1 39428350 39544345 - chr1 39492140 39492513 0 51832 . YES
+NM_018796_Eef1b2 chr1 63221360 63227060 + --- --- --- --- --- --- ---
+NM_018817_Smarcal1 chr1 72629842 72679806 + --- --- --- --- --- --- ---
+NM_018868_Nop58 chr1 59741819 59769026 + --- --- --- --- --- --- ---
+NM_018872_Tmem131 chr1 36841788 37000491 - --- --- --- --- --- --- ---
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+NM_019432_Tmem37 chr1 121962801 121979194 - --- --- --- --- --- --- ---
+NM_019445_Fmn2 chr1 176431685 176752860 + --- --- --- --- --- --- ---
+NM_019479_Hes6 chr1 93308097 93310595 - --- --- --- --- --- --- ---
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+NM_019562_Uchl5 chr1 145623774 145654586 + chr1 145591041 145591176 32598 32598 D NO
+NM_019570_Rev1 chr1 38109638 38186507 - --- --- --- --- --- --- ---
+NM_019645_Pkp1 chr1 137767972 137815881 - --- --- --- --- --- --- ---
+NM_019685_Ruvbl1 chr1 141824644 141826247 - --- --- --- --- --- --- ---
+NM_019759_Dpt chr1 166726785 166754377 + --- --- --- --- --- --- ---
+NM_019777_Ikbke chr1 133151052 133176163 - chr1 133114860 133115015 36037 61148 U NO
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+NM_019993_Aldh9a1 chr1 169280142 169298663 + --- --- --- --- --- --- ---
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+NM_020588_Tmem183a chr1 136242675 136258707 - --- --- --- --- --- --- ---
+NM_020604_Jph1 chr1 16837549 17087942 - chr1 17030405 17030545 0 57397 . YES
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+NM_021380_Il20 chr1 132803344 132808275 - --- --- --- --- --- --- ---
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+NM_021408_Ush2a chr1 190085902 190292167 + --- --- --- --- --- --- ---
+NM_021421_Angel2 chr1 192748297 192770827 + --- --- --- --- --- --- ---
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+NM_021600_Chrnd chr1 89087192 89096645 + --- --- --- --- --- --- ---
+NM_021605_Nek7 chr1 140379472 140516775 - --- --- --- --- --- --- ---
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+NM_022327_Ralb chr1 121363651 121401351 - --- --- --- --- --- --- ---
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+NM_025321_Sdhc chr1 173057297 173080736 - --- --- --- --- --- --- ---
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+NM_026321_Fam174a chr1 97174825 97346168 + --- --- --- --- --- --- ---
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+NM_028333_Angptl1 chr1 158769061 158791209 + chr1 158835251 158835391 44042 66190 U NO
+NM_028399_Ccnt2 chr1 129670253 129704638 + --- --- --- --- --- --- ---
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+NM_028450_Gulp1 chr1 44608366 44896390 + --- --- --- --- --- --- ---
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+NM_028713_Rftn2 chr1 55227030 55283748 - chr1 55283572 55283675 0 73 . YES
+NM_028717_Als2 chr1 59219131 59294111 - --- --- --- --- --- --- ---
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+NM_028776_Scyl3 chr1 165859251 165885242 + --- --- --- --- --- --- ---
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+NM_029398_Tmem14a chr1 21143538 21220248 + --- --- --- --- --- --- ---
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+NM_198899_Ugcgl1 chr1 36196873 36301555 - --- --- --- --- --- --- ---
+NM_198934_Pou2f1 chr1 167804181 167932753 - chr1 167906284 167906554 0 26199 . YES
+NM_199007_Sgol2 chr1 58026657 58085164 + --- --- --- --- --- --- ---
+NM_199021_Dpp10 chr1 125044486 126749525 - --- --- --- --- --- --- ---
+NM_201363_Serpinb3c chr1 109088051 109198931 - --- --- --- --- --- --- ---
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+NM_201641_Ugt1a10 chr1 89922380 90115570 + chr1 89989553 89989714 0 67173 . YES
+NM_206896_Olfr12 chr1 94516341 94538591 + --- --- --- --- --- --- ---
+NM_207031_Ano7 chr1 95270385 95302271 + chr1 95186508 95186637 83748 83748 D NO
+NM_207137_Olfr417 chr1 176299050 176299979 + --- --- --- --- --- --- ---
+NM_207137_Olfr417 chr1 176321202 176322113 + --- --- --- --- --- --- ---
+NM_207158_Olfr427 chr1 176028781 176030538 + --- --- --- --- --- --- ---
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+NM_207228_Tsga10 chr1 37783457 37922148 - --- --- --- --- --- --- ---
+NM_207233_C1ql2 chr1 122196386 122239751 + --- --- --- --- --- --- ---
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+NM_207583_Fam5b chr1 160175402 160286644 - --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58768296 58813658 + --- --- --- --- --- --- ---
+NM_207653_Cflar chr1 58813703 58815725 + --- --- --- --- --- --- ---
+NM_213616_Atp2b4 chr1 135602265 135697538 - chr1 135582677 135582828 19437 114710 U NO
+NR_002840_Gas5 chr1 162964758 162968663 + --- --- --- --- --- --- ---
+NR_002858_EG241041 chr1 21268965 21306401 - --- --- --- --- --- --- ---
+NR_002870_Dnm3os chr1 164119785 164155671 + chr1 164215623 164215935 59952 95838 U NO
+NR_003623_EG277333 chr1 182251970 182262902 - --- --- --- --- --- --- ---
+NR_026896_4931440L10Rik chr1 136437533 136449760 - --- --- --- --- --- --- ---
diff -r 000000000000 -r 0abe6bac47a6 test-data/rnachipintegrator_canonical_genes.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnachipintegrator_canonical_genes.loc Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,1 @@
+mm9_test mm9 mm9 ${__HERE__}/mm9_canonical_genes.tsv
diff -r 000000000000 -r 0abe6bac47a6 test-data/summits.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summits.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,654 @@
+#peak mid plus1
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diff -r 000000000000 -r 0abe6bac47a6 test-data/summits.xlsx
Binary file test-data/summits.xlsx has changed
diff -r 000000000000 -r 0abe6bac47a6 test-data/summits_per_feature.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/summits_per_feature.out Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,957 @@
+#gene.id gene.chr gene.start gene.end gene.strand chr_1 start_1 end_1 dist_closest_1 dist_TSS_1 direction_1 in_the_gene_1 chr_2 start_2 end_2 dist_closest_2 dist_TSS_2 direction_2 in_the_gene_2 chr_3 start_3 end_3 dist_closest_3 dist_TSS_3 direction_3 in_the_gene_3 chr_4 start_4 end_4 dist_closest_4 dist_TSS_4 direction_4 in_the_gene_4
+AF064749_Col6a3 chr1 92566771 92800755 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK015559_4930472D16Rik chr1 25020851 25021989 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK030377_A330023F24Rik chr1 196781953 196826186 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK080193_A530079E22Rik chr1 89401837 89403491 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+AK082264_C230030N03Rik chr1 34735043 34781084 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC006931_AI597479 chr1 43153807 43172843 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC021773_Glb1l chr1 75193364 75207353 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC023951_D1Ertd622e chr1 99540054 99558631 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC028767_3110009E18Rik chr1 122017764 122114603 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC031781_BC031781 chr1 182781250 182798240 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC034187_BC035947 chr1 78493611 78497758 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC043098_Fam168b chr1 34870072 34917183 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC049091_D1Bwg0212e chr1 39592545 39603734 + chr1 39502327 39502328 90217 90217 D NO . . . . . . . . . . . . . . . . . . . . .
+BC049713_Ankrd45 chr1 163072817 163099826 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC050813_4921511C04Rik chr1 37157481 37244861 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC051128_4921521F21Rik chr1 65059273 65079312 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC052693_2810422O20Rik chr1 165924541 165927371 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC052931_A630001G21Rik chr1 87601462 87674840 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC053100_5730559C18Rik chr1 138110108 138130841 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC054802_9630058J23Rik chr1 181476521 181558044 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC055845_2810025M15Rik chr1 159342483 159350353 + chr1 159250801 159250802 91681 91681 D NO . . . . . . . . . . . . . . . . . . . . .
+BC055955_A130010J15Rik chr1 194999663 195004015 + chr1 194967560 194967561 32102 32102 D NO . . . . . . . . . . . . . . . . . . . . .
+BC057872_Rab3gap2 chr1 187028006 187110623 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC058417_2610017I09Rik chr1 42648822 42751667 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC059254_Phlpp chr1 108042052 108306367 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC070435_Fam123c chr1 34620070 34671545 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC070446_Fam135a chr1 24017617 24107170 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC071241_9430016H08Rik chr1 57463192 57497936 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC072639_2010300C02Rik chr1 37646877 37776659 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC080290_5033414K04Rik chr1 84032539 84360735 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC082310_9430031J16Rik chr1 81073525 81338329 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC089525_2310007B03Rik chr1 95047933 95063386 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC089561_Cep350 chr1 157692096 157820375 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC147491_A230074B11Rik chr1 37083441 37133840 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+BC147657_9630028B13Rik chr1 187253234 187265698 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000027997_Rgs5 chr1 171625108 171625913 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000051203_1700001G17Rik chr1 33726669 33727551 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000054333_A130050O07Rik chr1 139823828 139826840 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000056879_C230029F24Rik chr1 49301475 49397265 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000057543_A730013G03Rik chr1 194659323 194661397 - chr1 194655297 194655298 4025 6099 U NO . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000062637_4930470H14Rik chr1 175156866 175201240 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000070048_ENSMUSG00000056128 chr1 92571736 92576368 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000070987_EG433384 chr1 183781705 183783320 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000072395_Olfr1406 chr1 175113651 175120746 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000094288_Wdr64 chr1 177654798 177798070 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000094950_Pgap1 chr1 54529849 54614539 - chr1 54641754 54641755 27215 27215 D NO . . . . . . . . . . . . . . . . . . . . .
+ENSMUST00000097776_Cnnm3 chr1 36567938 36585164 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+EU429481_Igfn1 chr1 137825893 137890307 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+FJ024495_Ildr2 chr1 168236882 168239692 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+FJ210934_Unc80 chr1 66514856 66556109 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001001565_Chpf chr1 75470923 75476437 - chr1 75491987 75491988 15550 15550 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_001001809_Olfr218 chr1 175130421 175134469 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001001883_Hecw2 chr1 53867026 54252002 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001003917_Atg9a chr1 75177439 75189181 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001004173_Sgpp2 chr1 78306692 78416864 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001005423_Mreg chr1 72170192 72258895 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001005507_Smg7 chr1 154684125 154750410 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001005508_Arhgap30 chr1 173319072 173340822 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001005520_Olfr244 chr1 176032571 176067605 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001008419_Aox3l1 chr1 58335180 58437083 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001008426_EG433365 chr1 155721475 155724001 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001008533_Adora1 chr1 136095799 136181661 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001009940_Il19 chr1 132786042 132915234 - chr1 132961088 132961089 45854 45854 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_001011525_Olfr1415 chr1 94376258 94381054 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001011525_Olfr1415 chr1 94407669 94418761 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001011684_Nms chr1 38995917 39007113 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001011873_Xkr9 chr1 13658862 13691794 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001011874_Xkr4 chr1 3203722 3713108 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001012330_Zfp238 chr1 179359958 179380892 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001013374_Lman2l chr1 36362897 36502078 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001013382_Lrrc52 chr1 169375806 169397136 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001013771_Gm973 chr1 59573136 59693241 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001013779_Aim2 chr1 175385835 175396165 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001014974_Ttll4 chr1 74708314 74748400 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001024721_BC094916 chr1 175451304 175466101 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001024945_Qsox1 chr1 157625296 157670499 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001025156_Ccdc93 chr1 123208865 123403037 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001025565_Lhx9 chr1 140694768 140740509 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001025602_Il1rl1 chr1 40462708 40522260 + chr1 40336020 40336021 126687 126687 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_001029984_Fcrlb chr1 172836813 172843072 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001037170_Tomm40l chr1 173147934 173152645 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001037725_Fam117b chr1 59937517 60042190 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001037918_Lipt1 chr1 37928603 37934232 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001037999_Dbi chr1 122009883 122046068 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001038592_Glrx2 chr1 145585774 145608282 + chr1 145601109 145601110 0 15335 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_001038619_Dnm3 chr1 163902671 164408155 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039126_Asb1 chr1 93437143 93461729 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039472_Kif21b chr1 138027986 138074578 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039475_Slco6b1 chr1 98802763 98894139 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039482_Klhl20 chr1 163018528 163061699 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039483_Tmco1 chr1 169238419 169279112 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039484_Kcnj10 chr1 174258852 174304216 + chr1 174386565 174386566 82349 127713 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_001039493_Plekhm3 chr1 64832557 65032270 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039495_Ccdc108 chr1 74947239 74982168 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039509_Pnkd chr1 74331504 74400245 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039710_Coq10b chr1 55101051 55129538 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001039934_Mtap2 chr1 66187374 66489157 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001042634_Clk1 chr1 58467034 58480936 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001045481_Ifi203 chr1 175804708 175928457 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001077189_Fcgr2b chr1 172890316 172916060 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001077353_Gsta3 chr1 21230690 21255722 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001077403_Nrp2 chr1 62724499 63100251 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081023_Cacna1s chr1 137949297 138016348 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081078_Lct chr1 130174327 130224881 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081079_Ogfrl1 chr1 23278472 23451348 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081259_Mfsd7b chr1 192825304 192850534 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081275_1700009P17Rik chr1 173032694 173057075 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081361_Mosc1 chr1 186610666 186635172 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001081756_E030049G20Rik chr1 128277776 128727190 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001082573_Crygc chr1 65118108 65146863 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001083897_Mpzl1 chr1 167522314 167564669 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001085409_Steap3 chr1 122037552 122169282 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001099637_Cep170 chr1 178663793 178744307 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001103182_Lin9 chr1 182572002 182620816 + chr1 182489776 182489777 82225 82225 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_001105667_Dtymk chr1 95689006 95698492 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001110783_Ank1 chr1 77759424 77766452 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001110831_Dnpep chr1 75304471 75314673 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001111059_Cd34 chr1 196683888 196826273 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001111279_Wdfy1 chr1 79689958 79772698 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001111314_Ngef chr1 89373415 89470499 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001111316_Ptprc chr1 139959456 140088994 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001111320_Idh1 chr1 65185668 65233033 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001113394_Cd247 chr1 167711216 167807397 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001122685_Rhbdd1 chr1 82313047 82441937 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001126046_Fam178b chr1 36619544 36740008 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001128605_Psen2 chr1 182157140 182247499 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001128609_Dedd chr1 173258959 173273620 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001130174_Tnnt2 chr1 137732931 137748838 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001134829_Lpgat1 chr1 193521144 193605705 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001136070_Lgtn chr1 133049773 133084235 + chr1 133124938 133124939 40703 75165 U NO chr1 132961088 132961089 88684 88684 D NO . . . . . . . . . . . . . .
+NM_001142647_Tmem194b chr1 52687569 52708760 + chr1 52635488 52635489 52080 52080 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_001159649_Lax1 chr1 135575626 135586665 - chr1 135592753 135592754 6088 6088 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_001159719_Sept2 chr1 95375046 95406820 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_001159730_Pdc chr1 152154402 152181077 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007381_Acadl chr1 66861363 66909886 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007415_Parp1 chr1 182499033 182531385 + chr1 182489776 182489777 9256 9256 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_007422_Adss chr1 179693113 179888685 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007432_Akp3 chr1 89021583 89042994 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007433_Akp5 chr1 88983274 88986861 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007453_Prdx6 chr1 163170243 163210238 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007463_Speg chr1 75371872 75428879 + chr1 75491987 75491988 63108 120115 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_007495_Astn1 chr1 160292424 160626748 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007498_Atf3 chr1 192994178 193057173 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007525_Bard1 chr1 71076934 71149526 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007561_Bmpr2 chr1 59820296 59927706 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007570_Btg2 chr1 135971251 135991759 - chr1 135862036 135862037 109214 129722 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_007576_C4bp chr1 132531357 132558199 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007642_Cd28 chr1 60763315 60830749 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007649_Cd48 chr1 173603288 173635385 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007685_Cfc1 chr1 34592493 34601156 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007695_Chi3l1 chr1 136069840 136086738 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007722_Cxcr7 chr1 92100063 92112863 + chr1 92080342 92080343 19720 19720 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_007733_Col19a1 chr1 24258667 24602262 - chr1 24619593 24619594 17331 17331 D NO chr1 24619958 24619959 17696 17696 D NO . . . . . . . . . . . . . .
+NM_007734_Col4a3 chr1 82583506 82718629 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007735_Col4a4 chr1 82438140 82584744 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007737_Col5a2 chr1 45431177 45560226 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007740_Col9a1 chr1 24164692 24268636 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007758_Cr2 chr1 196963005 197003002 - chr1 197067820 197067821 64818 64818 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_007768_Crp chr1 174620782 174763152 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007774_Cryga chr1 65146986 65150012 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007776_Crygd chr1 65108417 65110024 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007777_Cryge chr1 65095133 65097767 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007791_Csrp1 chr1 137526251 137648807 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007799_Ctse chr1 133534879 133572077 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007827_Daf2 chr1 132285116 132319576 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007842_Dhx9 chr1 155302618 155334755 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007853_Degs1 chr1 184205901 184212915 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007921_Elf3 chr1 137149649 137155139 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007923_Elk4 chr1 133904204 133929189 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_007936_Epha4 chr1 77280640 77511653 - chr1 77467717 77467718 0 43935 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_007955_Ptprv chr1 137004306 137029151 - chr1 136966533 136966534 37772 62617 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_007976_F5 chr1 166081877 166150388 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008030_Fmo3 chr1 164883934 164914811 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008057_Fzd7 chr1 59538966 59546428 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008059_G0s2 chr1 195098362 195108977 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008131_Glul chr1 155746721 155757023 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008132_Glrp1 chr1 90396446 90406631 - chr1 90423032 90423033 16401 16401 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_008209_Mr1 chr1 156951231 157006024 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008210_H3f3a chr1 182694052 182744054 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008250_Hlx chr1 186542564 186592227 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008288_Hsd11b1 chr1 195047814 195090228 - chr1 194967560 194967561 80253 122667 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_008299_Dnajb3 chr1 90101307 90102337 - chr1 89999634 89999635 101672 102702 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_008311_Htr2b chr1 87995611 88008576 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008327_Ifi202b chr1 175892699 175912872 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008329_Ifi204 chr1 175677424 175929523 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008342_Igfbp2 chr1 72840313 72899038 + chr1 72825630 72825631 14682 14682 D NO chr1 72780142 72780143 60170 60170 D NO chr1 72779940 72779941 60372 60372 D NO . . . . . . .
+NM_008362_Il1r1 chr1 40274145 40373439 + chr1 40336020 40336021 0 61875 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_008365_Il18r1 chr1 40522407 40557703 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008384_Inpp1 chr1 52826936 52890006 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008429_Kcnj9 chr1 174250632 174259434 - chr1 174386565 174386566 127131 127131 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_008440_Kif1a chr1 94912041 94998420 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008484_Lamb3 chr1 195033913 195170047 + chr1 194967560 194967561 66352 66352 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_008485_Lamc2 chr1 154969890 155033557 - chr1 154981623 154981624 0 51933 . YES chr1 155133374 155133375 99817 99817 D NO . . . . . . . . . . . . . .
+NM_008510_Xcl1 chr1 166861801 166916999 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008515_Lrrfip1 chr1 92895314 93025509 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008534_Ly9 chr1 173518153 173537531 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008551_Mapkapk2 chr1 132950274 133013820 - chr1 132961088 132961089 0 52731 . YES chr1 133124938 133124939 111118 111118 D NO . . . . . . . . . . . . . .
+NM_008563_Mcm3 chr1 20792654 20810343 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008567_Mcm6 chr1 130228167 130256262 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008575_Mdm4 chr1 134877138 134927144 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008623_Mpz chr1 173081953 173091254 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008651_Mybl1 chr1 9635825 9690280 - chr1 9629279 9629280 6545 61000 U NO chr1 9629107 9629108 6717 61172 U NO . . . . . . . . . . . . . .
+NM_008667_Nab1 chr1 52487127 52611216 - chr1 52635488 52635489 24272 24272 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_008678_Ncoa2 chr1 13129206 13399268 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008696_Map4k4 chr1 39958025 40102235 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008719_Npas2 chr1 39250631 39420071 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008763_Olfr16 chr1 174886928 174887857 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008765_Orc2l chr1 58519275 58561933 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008781_Pax3 chr1 78047196 78193701 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008795_Pctk3 chr1 133972174 134036519 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008798_Pdcd1 chr1 95931620 95977526 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008801_Pde6d chr1 88427331 88479102 - chr1 88419118 88419119 8212 59983 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_008825_Pfkfb2 chr1 132566787 132625820 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008866_Lypla1 chr1 4797815 4844373 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008869_Pla2g4a chr1 151661289 151808414 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008882_Plxna2 chr1 196411150 196654445 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008900_Pou3f3 chr1 42662066 42757055 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008911_Ppox chr1 173200042 173211335 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008922_Prim2 chr1 33510658 33727287 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008937_Prox1 chr1 191943166 191999411 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008976_Ptpn14 chr1 191512039 191694746 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008985_Ptprn chr1 75243625 75261057 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008998_Rab17 chr1 92842177 92905581 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_008999_Rab23 chr1 33776747 33799402 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009049_Resp18 chr1 75268774 75274970 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009061_Rgs2 chr1 145846468 145858945 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009062_Rgs4 chr1 171671620 171743114 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009063_Rgs5 chr1 171585632 171625107 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009107_Rxrg chr1 169399669 169569753 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009118_Sag chr1 89700275 89741733 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009126_Serpinb3a chr1 108942184 108948902 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009129_Scg2 chr1 79431244 79436675 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009183_St8sia4 chr1 97484259 97672426 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009190_Vps4b chr1 108665873 108739123 - chr1 108757655 108757656 18532 18532 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_009208_Slc4a3 chr1 75539833 75564973 + chr1 75491987 75491988 47845 47845 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_009230_Soat1 chr1 158354679 158417632 - chr1 158520668 158520669 103036 103036 D NO chr1 158547339 158547340 129707 129707 D NO . . . . . . . . . . . . . .
+NM_009255_Serpine2 chr1 79778648 79891246 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009257_Serpinb5 chr1 108757652 108779925 + chr1 108757655 108757656 0 3 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_009283_Stat1 chr1 51740305 52218707 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009307_Syt2 chr1 136543209 136659150 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009334_Tcfap2b chr1 19198995 19228906 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009352_Terf1 chr1 15785995 15845901 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009355_Tesp1 chr1 34554997 34559905 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009356_Tesp2 chr1 34594321 34617749 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009367_Tgfb2 chr1 188337162 188544530 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009399_Tnfrsf11a chr1 107677300 107859295 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009407_Tnp1 chr1 73061657 73062512 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009418_Tpp2 chr1 43936027 44065003 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009447_Tuba4a chr1 75210818 75219831 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009452_Tnfsf4 chr1 163212600 163374314 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009460_Sumo1 chr1 59643412 59727658 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009480_Usf1 chr1 173341335 173348954 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009509_Vil1 chr1 74455970 74485488 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009518_Wnt10a chr1 74838090 74898253 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009526_Wnt6 chr1 74818493 74831875 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009533_Xrcc5 chr1 72354001 72453365 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009539_Zap70 chr1 36818663 36839663 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009579_Slc30a1 chr1 193730666 193737101 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009581_Zp3r chr1 132473290 132526179 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009604_Chrng chr1 89102267 89109269 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009676_Aox1 chr1 58086687 58165423 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009721_Atp1b1 chr1 166367243 166524675 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009741_Bcl2 chr1 108362593 108614036 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009782_Cacna1e chr1 156242220 156916799 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009786_Cacybp chr1 162132500 162143003 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009791_Aspm chr1 141351360 141393207 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009794_Capn2 chr1 184394108 184479307 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009803_Nr1i3 chr1 173122612 173149661 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009812_Casp8 chr1 58818409 58904327 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009813_Casq1 chr1 174140028 174150006 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009826_Rb1cc1 chr1 6196277 6266709 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009843_Ctla4 chr1 60943864 61098205 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009872_Cdk5r2 chr1 74901511 74904288 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009909_Il8rb chr1 74200075 74207820 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009911_Cxcr4 chr1 130436268 130609324 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009918_Cnga3 chr1 37275192 37321882 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009930_Col3a1 chr1 45368295 45413500 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_009938_Copa chr1 174012565 174052450 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010016_Cd55 chr1 132326379 132359520 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010043_Des chr1 75356887 75365134 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010045_Darc chr1 175234342 175263520 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010094_Lefty1 chr1 182865132 182868532 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010098_Opn3 chr1 177592560 177622774 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010133_En1 chr1 122494080 122540975 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010135_Enah chr1 183776371 183949877 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010145_Ephx1 chr1 182919689 182951015 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010164_Eya1 chr1 14117632 14318907 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010177_Fasl chr1 163710820 163718844 - chr1 163837980 163837981 119136 119136 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_010184_Fcer1a chr1 175148098 175157377 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010185_Fcer1g chr1 173159708 173164476 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010188_Fcgr3 chr1 172916162 173015807 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010209_Fh1 chr1 177427308 177555746 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010212_Fhl2 chr1 43179941 43255166 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010231_Fmo1 chr1 164744557 164796721 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010233_Fn1 chr1 71632113 71736637 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010262_Gbx2 chr1 91824531 91831059 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010267_Gdap1 chr1 17135463 17385513 + chr1 17040475 17040476 94987 94987 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_010341_Nmur1 chr1 88282479 88297441 - chr1 88419118 88419119 121677 121677 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_010472_Agfg1 chr1 82836048 82918151 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010476_Hsd17b7 chr1 171879671 171899542 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010483_Htr5b chr1 123406263 123425032 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010500_Ier5 chr1 156943491 156946949 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010518_Igfbp5 chr1 72904507 72921468 - chr1 72825630 72825631 78876 95837 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_010544_Ihh chr1 74991633 75093213 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010548_Il10 chr1 132916424 132921547 + chr1 132961088 132961089 39541 44664 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_010552_Il17a chr1 20660053 20766059 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010553_Il18rap chr1 40572207 40606867 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010555_Il1r2 chr1 40130058 40182052 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010564_Inha chr1 75503647 75506924 + chr1 75491987 75491988 11659 11659 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_010566_Inpp5d chr1 89504177 89645401 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010570_Irs1 chr1 82229682 82233665 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010570_Irs1 chr1 82229686 82300552 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010584_Itln1 chr1 173448254 173495879 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010600_Kcnh1 chr1 194014507 194368391 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010607_Kcnk2 chr1 191031813 191229415 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010629_Kifap3 chr1 165671988 165847216 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010633_Uhmk1 chr1 172123558 172145524 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010678_Aff3 chr1 38232856 38782360 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010683_Lamc1 chr1 155065803 155179906 - chr1 155133374 155133375 0 46531 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_010712_Lhx4 chr1 157520057 157598794 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010732_Lrrn2 chr1 134776870 134865321 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010766_Marco chr1 122261022 122466383 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010778_Cd46 chr1 196861976 196919007 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010827_Msc chr1 14520272 14746075 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010834_Mstn chr1 53118495 53124923 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010863_Myo1b chr1 51806622 51973696 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010865_Myoc chr1 164569268 164581467 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010879_Nck2 chr1 43501442 43627345 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010880_Ncl chr1 88241155 88255995 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010892_Nek2 chr1 193645343 193656921 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010916_Nhlh1 chr1 173982425 173987707 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_010933_Nppc chr1 88512597 88567147 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011011_Oprk1 chr1 5578025 5596202 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011063_Pea15a chr1 174126043 174136915 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011066_Per2 chr1 93312559 93386413 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011070_Pfdn2 chr1 173275115 173289384 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011082_Pigr chr1 132723238 132748826 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011086_Pikfyve chr1 65225807 65332228 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011111_Serpinb2 chr1 109407675 109422169 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011198_Ptgs2 chr1 151947054 152026155 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011206_Ptpn18 chr1 34516613 34532568 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011267_Rgs16 chr1 155574693 155592596 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011273_Xpr1 chr1 157103002 157264554 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011277_Rnf2 chr1 153305192 153359013 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011283_Rp1 chr1 3989638 4469288 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011318_Apcs chr1 174824092 174855560 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011345_Sele chr1 165978323 165988607 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011346_Sell chr1 165992132 166007817 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011347_Selp chr1 166045416 166080154 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011439_Sox13 chr1 135278853 135384763 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011441_Sox17 chr1 4481009 4487839 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011459_Serpinb8 chr1 109486542 109586251 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011465_Spna1 chr1 176102906 176178561 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011487_Stat4 chr1 52036485 52164030 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011494_Stk16 chr1 75207414 75212181 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011541_Tcea1 chr1 4847584 4889703 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011590_Timm17a chr1 137197272 137210335 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011633_Traf5 chr1 193821096 193916369 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011650_Tsn chr1 120194658 120208016 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011729_Ercc5 chr1 44204270 44256568 + chr1 44205544 44205545 0 1274 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_011770_Ikzf2 chr1 69574124 69733875 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011780_Adam23 chr1 63482194 63639230 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011780_Adam23 chr1 63640970 63642850 + chr1 63674953 63674954 32103 33983 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_011785_Akt3 chr1 178940936 179188314 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011794_Bpnt1 chr1 187156058 187181696 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011796_Capn10 chr1 94830953 94844518 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011800_Cdh20 chr1 106665116 106892058 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011804_Creg1 chr1 167693878 167710825 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011811_Farsb chr1 78414533 78506689 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011825_Grem2 chr1 176763926 176859770 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011880_Rgs7 chr1 176989221 177422985 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011882_Rnasel chr1 155596576 155619417 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011931_Rfwd2 chr1 161159948 161307408 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_011935_Esrrg chr1 189432683 190062059 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_012009_Sh2d1b1 chr1 172162900 172220030 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_012012_Exo1 chr1 177810732 177841721 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_012049_Nit1 chr1 173270709 173276021 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_012058_Srp9 chr1 183988019 184062514 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013474_Apoa2 chr1 173151908 173156502 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013489_Cd84 chr1 173769848 173820852 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013499_Cr1l chr1 196924298 196957754 - chr1 197067820 197067821 110066 110066 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_013612_Slc11a1 chr1 74421758 74433050 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013626_Pam chr1 99691711 100053468 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013673_Sp100 chr1 84943347 87618694 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013715_Cops5 chr1 10014683 10028315 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013729_Mixl1 chr1 182623184 182634680 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013730_Slamf1 chr1 173682982 173731471 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013750_Phlda3 chr1 137662671 137665710 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013784_Pign chr1 107385512 107560244 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013835_Trove2 chr1 145597816 145624178 - chr1 145601109 145601110 0 23068 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_013862_Rabgap1l chr1 162149308 162739582 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_013919_Usp21 chr1 173212080 173218102 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_015750_Neu2 chr1 89348720 89494397 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_015780_Cfhr1 chr1 141443639 141456806 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_015811_Rgs1 chr1 146060709 146118313 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_015818_Hs6st1 chr1 36125255 36163289 + chr1 36116936 36116937 8318 8318 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_016696_Gpc1 chr1 94728253 94757346 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016702_Agxt chr1 95031777 95041991 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016716_Cul3 chr1 80261498 80323399 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016717_Scly chr1 93192544 93217635 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016749_Mybph chr1 136090025 136097809 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016778_Bok chr1 95579016 95592340 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016796_Vamp4 chr1 164500371 164532593 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016805_Hnrnpu chr1 180251245 180298730 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016846_Rgl1 chr1 154357421 154613475 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016851_Irf6 chr1 194979326 194998230 + chr1 194967560 194967561 11765 11765 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_016894_Ramp1 chr1 93076419 93120251 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016894_Ramp1 chr1 93120257 93121772 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016916_Blcap chr1 46068602 46087314 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016917_Slc40a1 chr1 45964925 45999090 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016923_Ly96 chr1 16678152 16699618 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016928_Tlr5 chr1 184884929 184903333 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_016960_Ccl20 chr1 83112527 83138624 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_017480_Icos chr1 61034747 61057162 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018729_Cd244 chr1 173481630 173515439 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018750_Rassf5 chr1 133072991 133144761 - chr1 133124938 133124939 0 19822 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_018775_Tbc1d8 chr1 39428350 39544345 - chr1 39502327 39502328 0 42017 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_018796_Eef1b2 chr1 63221360 63227060 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018817_Smarcal1 chr1 72629842 72679806 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018868_Nop58 chr1 59741819 59769026 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018872_Tmem131 chr1 36841788 37000491 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_018881_Fmo2 chr1 164804452 164828875 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019432_Tmem37 chr1 121962801 121979194 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019445_Fmn2 chr1 176431685 176752860 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019479_Hes6 chr1 93308097 93310595 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019484_Refbp2 chr1 173433397 173434881 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019562_Uchl5 chr1 145623774 145654586 + chr1 145601109 145601110 22664 22664 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_019570_Rev1 chr1 38109638 38186507 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019645_Pkp1 chr1 137767972 137815881 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019685_Ruvbl1 chr1 141824644 141826247 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019759_Dpt chr1 166726785 166754377 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019777_Ikbke chr1 133151052 133176163 - chr1 133124938 133124939 26113 51224 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_019790_Tmeff2 chr1 50957501 51282275 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019933_Ptpn4 chr1 121556050 121771541 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_019993_Aldh9a1 chr1 169280142 169298663 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_020025_B3galt2 chr1 145487786 145497516 + chr1 145601109 145601110 103593 113323 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_020579_B4galt3 chr1 173199650 173207025 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_020588_Tmem183a chr1 136242675 136258707 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_020604_Jph1 chr1 16837549 17087942 - chr1 17040475 17040476 0 47466 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_021285_Myl1 chr1 66948125 66992032 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021295_Lancl1 chr1 67004053 67085447 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021306_Ecel1 chr1 89039384 89053076 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021312_Wdr12 chr1 60099363 60155552 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021313_Rnf25 chr1 74640329 74648026 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021342_Kcne4 chr1 78791793 78816579 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021350_Chml chr1 177615948 177618649 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021374_Rgs20 chr1 4899617 5060346 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021380_Il20 chr1 132803344 132808275 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021383_Rqcd1 chr1 74542393 74577404 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021400_Prg4 chr1 152296956 152333784 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021408_Ush2a chr1 190085902 190292167 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021421_Angel2 chr1 192748297 192770827 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021433_Stx6 chr1 157005819 157054716 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021467_Tnni1 chr1 137676021 137713725 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021511_Rrs1 chr1 9535513 9537532 + chr1 9629107 9629108 91575 93594 U NO chr1 9629279 9629280 91747 93766 U NO . . . . . . . . . . . . . .
+NM_021537_Stk25 chr1 95517348 95555233 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021541_Cryba2 chr1 74936508 74939802 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021600_Chrnd chr1 89087192 89096645 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021605_Nek7 chr1 140379472 140516775 - chr1 140391721 140391722 0 125053 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_021607_Ncstn chr1 173996154 174012927 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_021610_Gpa33 chr1 168060559 168118074 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022018_Fam129a chr1 153370940 153589282 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022019_Dusp10 chr1 185755009 185899515 + chr1 185865026 185865027 0 110017 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_022312_Tnr chr1 161327058 161857057 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022320_Gpr35 chr1 94683531 94882968 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022327_Ralb chr1 121363651 121401351 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022329_Ifrg15 chr1 157883344 157900866 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022417_Itm2c chr1 87780787 87838221 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022563_Ddr2 chr1 171907607 172040752 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022721_Fzd5 chr1 64777130 64826549 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022881_Rgs18 chr1 146599793 146755382 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_022988_Nif3l1 chr1 58501750 58538650 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023041_Pex19 chr1 174056859 174067189 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023141_Tor3a chr1 158583760 158604477 - chr1 158590699 158590700 0 13777 . YES chr1 158547339 158547340 36420 57137 U NO chr1 158520668 158520669 63091 83808 U NO . . . . . . .
+NM_023173_Dusp12 chr1 172803629 172815650 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023200_Ppp1r7 chr1 95239431 95266345 + chr1 95196573 95196574 42857 42857 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_023284_Nuf2 chr1 171386224 171461676 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023314_Eif4e2 chr1 89110486 89145136 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023341_Cabc1 chr1 182095369 182129713 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023343_Ilkap chr1 93270445 93290447 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023434_Tox4 chr1 16757104 16760219 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023514_Mrps9 chr1 42760822 42962528 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023523_Pecr chr1 72281105 72330878 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023617_Aox3 chr1 58169980 58259027 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023631_Aox4 chr1 58267261 58325441 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023645_Kdelc1 chr1 44143458 44177102 - chr1 44205544 44205545 28442 28442 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_023727_Rd3 chr1 193784705 193812153 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023732_Abcb6 chr1 75168223 75177000 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023755_Tcfcp2l1 chr1 120524515 120655075 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_023884_Ralgps2 chr1 158734300 158969600 - chr1 158845321 158845322 0 124278 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_024197_Ndufa10 chr1 94121208 94393553 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_024264_Cyp27a1 chr1 74759770 74786412 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_024282_Pppde1 chr1 180117558 180197483 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_024283_1500015O10Rik chr1 43787414 43799399 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025283_Mobkl3 chr1 55187734 55211736 + chr1 55293624 55293625 81888 105890 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_025300_Mrpl15 chr1 4763290 4798011 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025303_Stau2 chr1 16218775 16510193 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025321_Sdhc chr1 173057297 173080736 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025386_Fbxo36 chr1 84835492 84897059 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025388_Ufc1 chr1 173218698 173225135 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025424_Nenf chr1 193130454 193141997 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025439_Tmem9 chr1 137879942 137931919 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025453_Tm4sf20 chr1 82749860 82765031 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025454_Ing5 chr1 95700534 95719794 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025470_1810030J14Rik chr1 176260650 176349219 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025474_Mrps14 chr1 162082365 162131317 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025505_Blzf1 chr1 166219931 166237615 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025557_Pcp4l1 chr1 173103394 173126370 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025569_Mgst3 chr1 169302037 169323952 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025596_Prelid1 chr1 63410974 63469460 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025597_Ndufb3 chr1 58631453 58653239 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025677_Tsen15 chr1 154217920 154233812 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025683_Rpe chr1 66747223 66839854 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025746_4933415F23Rik chr1 23107346 23263222 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025773_Ube2w chr1 16530881 16609419 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025784_Bcs1l chr1 74634010 74639375 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025819_1200016B10Rik chr1 153214763 153304502 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025864_Tmem206 chr1 193149566 193176819 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025867_Serpinb11 chr1 109246610 109277052 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025920_Thap4 chr1 95602021 95651542 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_025964_Fam119a chr1 64653048 64670990 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026024_Ube2t chr1 136857731 136870739 + chr1 136966533 136966534 95794 108802 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_026041_Rrp15 chr1 188544857 188573732 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026078_Pigc chr1 163860747 163957217 + chr1 163837980 163837981 22766 22766 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_026123_Unc50 chr1 37486671 37504876 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026171_Nvl chr1 183008557 183074318 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026187_Ankzf1 chr1 75188977 75192143 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026187_Ankzf1 chr1 75192524 75195962 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026195_Atic chr1 71584010 71626205 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026234_Pigm chr1 174306609 174314210 + chr1 174386565 174386566 72355 79956 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_026241_Ankrd39 chr1 36594353 36604077 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026250_Zh2c2 chr1 99658035 99706130 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026321_Fam174a chr1 97174825 97346168 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026367_Gpatch2 chr1 189010707 189180483 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026369_Arpc5 chr1 154613024 154638792 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026375_Ahctf1 chr1 181675025 181733948 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026380_Rgs8 chr1 155468581 155563679 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026390_Ubxn4 chr1 130140557 130175951 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026430_Uxs1 chr1 43804890 43884625 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026454_Ube2f chr1 93146888 93187187 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026456_Tceb1 chr1 16603307 16655630 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026472_Mki67ip chr1 120218436 120230401 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026493_Cspp1 chr1 10028093 10126849 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026500_Ddx59 chr1 138242798 138336799 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026503_1110058L19Rik chr1 24002785 24017210 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026626_Efcab2 chr1 180335927 180414624 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026680_Golt1a chr1 135206322 135226478 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026713_Mogat1 chr1 78496730 78564215 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026719_Lmbrd1 chr1 24593456 24847969 + chr1 24619593 24619594 0 26137 . YES chr1 24619958 24619959 0 26502 . YES . . . . . . . . . . . . . .
+NM_026719_Lmbrd1 chr1 24820582 24823143 + chr1 24741037 24741038 79544 79544 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_026725_Dusp23 chr1 174560902 174563119 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026796_Smyd2 chr1 191704373 191746222 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026823_Arl8a chr1 137043216 137053347 + chr1 136966533 136966534 76682 76682 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_026846_Zfand2b chr1 75165237 75168196 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026850_Pdcl3 chr1 39044622 39054081 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026913_Mitd1 chr1 37931656 37947242 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_026977_1810031K17Rik chr1 75131500 75139270 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027098_Mrpl30 chr1 37947313 37959167 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027154_Tmbim1 chr1 74334823 74352176 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027159_Ccdc115 chr1 34491854 34496517 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027188_Smyd3 chr1 180885172 181448168 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027300_Spata3 chr1 87913403 87926533 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027351_Ppil3 chr1 58486110 58502330 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027357_Psmd1 chr1 87958636 88174849 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027407_Ica1l chr1 60039354 60099956 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027415_Tmem70 chr1 16610621 16668358 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027430_Brp44 chr1 167390752 167411345 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027534_Kdsr chr1 108617007 108656357 - chr1 108757655 108757656 101298 101298 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_027548_Serpinb7 chr1 109296172 109349266 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027551_Klhl30 chr1 93244259 93259068 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027637_4931428L18Rik chr1 31197921 31279501 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027661_Hsfy2 chr1 56668158 56822175 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027677_Gpr39 chr1 127573518 127795359 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027678_Zranb3 chr1 129846941 130025531 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027725_Wdr69 chr1 83156310 83207145 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027884_Tns1 chr1 73956820 74144891 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027886_Stk11ip chr1 75518100 75533910 + chr1 75491987 75491988 26112 26112 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_027893_Pvrl4 chr1 173292993 173318729 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027921_Slc16a14 chr1 84902046 84931841 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_027971_Serpinb12 chr1 108831026 108853655 + chr1 108757655 108757656 73370 73370 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_027979_Chit1 chr1 136007829 136048117 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028057_Cyb5r1 chr1 136302358 136308302 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028091_Osgepl1 chr1 53370488 53383184 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028135_Tmem163 chr1 129382910 129574703 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028173_Tram1 chr1 13554779 13579965 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028250_Acbd6 chr1 157358146 157536633 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028320_Adipor1 chr1 136311830 136329944 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028333_Angptl1 chr1 158769061 158791209 + chr1 158845321 158845322 54112 76260 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_028399_Ccnt2 chr1 129670253 129704638 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028408_Cnih3 chr1 183282759 183419790 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028450_Gulp1 chr1 44608366 44896390 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028534_Smap1 chr1 23833022 23929292 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028696_Obfc2a chr1 51417024 51550602 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028713_Rftn2 chr1 55227030 55283748 - chr1 55293624 55293625 9876 9876 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_028717_Als2 chr1 59219131 59294111 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028749_Npl chr1 155350145 155424001 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028776_Scyl3 chr1 165859251 165885242 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028776_Scyl3 chr1 165876143 165924907 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028778_Nuak2 chr1 134212715 134241254 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028787_Slc35f5 chr1 127332249 127554856 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028817_Acsl3 chr1 78654388 78743434 + chr1 78641027 78641028 13360 13360 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_028829_Paqr8 chr1 20811519 20929711 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028848_Spata17 chr1 188868366 189039831 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028889_Efhd1 chr1 89160561 89207413 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_028942_Slco6c1 chr1 98899133 99024880 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029025_Tmem81 chr1 134402623 134405216 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029084_Slamf8 chr1 174510275 174520700 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029115_4930455F23Rik chr1 166205721 166217973 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029160_Spag16 chr1 69873526 70771706 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029269_Spp2 chr1 90303568 90373213 + chr1 90423032 90423033 49819 119464 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_029398_Tmem14a chr1 21143538 21220248 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029409_Mff chr1 82721393 82748958 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029612_Slamf9 chr1 174392516 174408706 + chr1 174386565 174386566 5950 5950 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_029696_Mdh1b chr1 63745401 63776894 - chr1 63674953 63674954 70447 101940 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_029756_Sdccag8 chr1 178743478 178953256 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029766_Dtl chr1 193272523 193399423 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029846_Atg16l1 chr1 89652465 89697344 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_029888_Zfp142 chr1 74612492 74634794 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030013_Cyp20a1 chr1 60400175 60444904 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030025_Ccdc150 chr1 54251865 54451794 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030060_Batf3 chr1 192921746 192944913 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030131_Cnih4 chr1 183074401 183099213 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030211_Kctd18 chr1 58007830 58075790 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030245_Tada1l chr1 168309248 168323752 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030266_Inpp4a chr1 37356703 37476203 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030556_Slc19a3 chr1 83001155 83083196 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030676_Nr5a2 chr1 138739149 138950879 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030710_Slamf6 chr1 173847613 173932462 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_030724_Uck2 chr1 169106790 169215431 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_031164_F13b chr1 141398326 141420329 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_031179_Sf3b1 chr1 55042016 55084369 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_031189_Myog chr1 136186558 136189125 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_031192_Ren1 chr1 135246578 135256895 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_031402_Crispld1 chr1 17717123 17756425 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_032005_Tbx19 chr1 167056323 167090894 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_033077_D1Pas1 chr1 188791295 188934742 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_033509_Vangl2 chr1 173931096 173977129 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_033563_Klf7 chr1 64049920 64169179 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_033570_Cnnm4 chr1 36528452 36565609 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_033608_Igsf9 chr1 174411686 174429005 + chr1 174386565 174386566 25120 25120 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_033652_Lmx1a chr1 169579767 169778872 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053015_Mlph chr1 92811657 92847814 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053095_Il24 chr1 132778072 132784021 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053106_Lmod1 chr1 137221395 137264642 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053107_Gpr45 chr1 43009719 43092301 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053191_Pi15 chr1 17591992 17621000 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053199_Cadm3 chr1 175264723 175362523 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_053257_Rpl31 chr1 39421000 39429094 + chr1 39502327 39502328 73233 81327 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_053270_Rims1 chr1 22275987 22813178 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_054076_Optc chr1 135787973 135805299 - chr1 135862036 135862037 56737 56737 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_054077_Prelp chr1 135806855 135865173 - chr1 135862036 135862037 0 3136 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_054087_Slc19a2 chr1 166178694 166196022 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_054102_Ivns1abp chr1 153196503 153212127 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_080419_Igsf8 chr1 174191772 174249967 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_080844_Serpinc1 chr1 162908738 162946004 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_080850_Pask chr1 95205357 95240039 - chr1 95196573 95196574 8783 43465 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_130456_Nphs2 chr1 158233397 158258162 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_130890_Capn8 chr1 184489366 184629001 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133193_Il1rl2 chr1 40381454 40447345 + chr1 40336020 40336021 45433 45433 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_133220_Sgk3 chr1 9787936 9890911 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133225_Acbd3 chr1 182654006 182684317 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133235_Khdrbs2 chr1 32113056 32771277 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133239_Crb1 chr1 141093643 141296750 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133252_Tram2 chr1 20984161 21069306 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133358_Zfp617 chr1 87909957 87912999 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133664_Lad1 chr1 137715163 137730085 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133684_Mosc2 chr1 186636947 186687141 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133705_Pycr2 chr1 182834431 182850616 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133728_Asnsd1 chr1 53382361 53409576 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133748_Insig2 chr1 123200933 123229157 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133780_Tpr chr1 152239968 152298193 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133781_Cab39 chr1 87687678 87748148 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133805_Cops8 chr1 92499556 92564446 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133806_Uap1 chr1 172007106 172105098 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133808_Hdlbp chr1 95302520 95375513 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133809_Kmo chr1 177550532 177592237 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133810_Stk17b chr1 53812356 53857070 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133815_Lbr chr1 183737722 183773157 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133816_Sh3bp4 chr1 90966984 91051778 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133817_Zfp451 chr1 33817052 33871530 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133819_Ppp1r15b chr1 135027595 135036355 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133826_Atp6v1h chr1 5060109 5173662 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133828_Creb1 chr1 64579391 64645546 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133828_Creb1 chr1 64646684 64649524 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133829_Mfsd6 chr1 52702101 52784383 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133832_Rdh10 chr1 16095419 16123815 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_133975_Trip12 chr1 84717781 84836834 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_134252_Trpm8 chr1 90181363 90285482 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_134438_Gpr37l1 chr1 137054243 137069087 - chr1 136966533 136966534 87709 102553 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_134448_Dst chr1 33965107 34411632 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_138314_Nme7 chr1 166237503 166369483 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_138741_Sdpr chr1 51345970 51359791 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_139146_Satb2 chr1 56850830 57044309 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_139150_Carf chr1 60155057 60208366 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_139152_Asb18 chr1 91849253 91911152 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_139270_Pth2r chr1 65328648 65436194 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144530_Zc3h11a chr1 135516445 135557956 - chr1 135592753 135592754 34797 34797 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_144539_Slamf7 chr1 173562534 173583396 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144558_Bivm chr1 44175822 44201615 + chr1 44205544 44205545 3929 29722 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_144559_Fcgr4 chr1 172925278 172974678 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144761_Crygb chr1 65126809 65127141 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144791_Tor1aip1 chr1 157851734 157889804 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144794_Tmem63a chr1 182872430 182919700 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144796_Susd4 chr1 184694011 184850523 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144810_Klhdc8a chr1 134182914 134204342 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144814_Rcor3 chr1 193910981 193962565 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144817_Camk1g chr1 195172540 195216632 - chr1 195334592 195334593 117960 117960 D NO chr1 195340816 195340817 124184 124184 D NO . . . . . . . . . . . . . .
+NM_144875_Rab7l1 chr1 133763813 133782396 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144877_Mettl13 chr1 164462268 164478659 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144878_Fmo4 chr1 164675648 164744002 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144879_Vash2 chr1 192771545 192803413 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144880_Ppp2r5a chr1 193175865 193290728 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144881_Hhat chr1 194320603 194649833 - chr1 194655297 194655298 5464 5464 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_144882_2810022L02Rik chr1 57831026 58005952 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144953_1700019D03Rik chr1 52981207 53077002 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_144960_Fcamr chr1 132697479 132711317 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145100_Lypd1 chr1 127768620 127809650 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145128_Mgat5 chr1 129101583 129384133 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145141_Fcrla chr1 172847725 172857714 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145142_Chst10 chr1 38920721 38955057 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145143_Mpp4 chr1 59177791 59218762 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145222_B3gnt7 chr1 88199427 88203870 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145381_Lactb2 chr1 13604244 13650616 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145392_Bag2 chr1 33802345 33814648 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145413_Fam20b chr1 158608676 158649180 - chr1 158590699 158590700 17976 58480 U NO chr1 158547339 158547340 61336 101840 U NO chr1 158520668 158520669 88007 128511 U NO . . . . . . .
+NM_145415_AA408296 chr1 194918802 194956446 - chr1 194967560 194967561 11114 11114 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_145417_Rnpep chr1 137159304 137180985 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145506_Epb4.1l5 chr1 121437741 121545557 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145508_Dyrk3 chr1 133018921 133034897 - chr1 132961088 132961089 57832 73808 U NO chr1 133124938 133124939 90041 90041 D NO . . . . . . . . . . . . . .
+NM_145509_5430435G22Rik chr1 133585272 133610099 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145510_Rabif chr1 136391105 136405512 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145511_BC003331 chr1 152183263 152240229 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145512_Sft2d2 chr1 167104119 167124549 - chr1 167233113 167233114 108564 108564 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_145513_Tiprl chr1 167133855 167183116 - chr1 167233113 167233114 49997 49997 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_145514_Wdr26 chr1 183100306 183150525 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145515_Mark1 chr1 186720345 186823408 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145516_Plekhb2 chr1 34906787 34936422 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145517_Ormdl1 chr1 53353438 53367153 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145518_Ndufs1 chr1 63190187 63223454 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145519_Farp2 chr1 95408676 95518914 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145624_Zfp709 chr1 87911157 87911749 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145692_Lrrc67 chr1 9943781 9999420 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145856_Il17f chr1 20767237 20776566 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145977_Slc45a3 chr1 133859512 133879541 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_145991_Cdc73 chr1 145274292 145549936 - chr1 145601109 145601110 51173 51173 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_145996_Arid5a chr1 36359349 36380874 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146103_Tmem185b chr1 121396063 121425550 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146106_Lyplal1 chr1 187911630 187941208 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146107_Actr1b chr1 36754975 36766847 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146108_Hibch chr1 52899113 52977830 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146110_Aamp chr1 74326421 74331613 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146112_Gigyf2 chr1 89223593 89347370 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146250_Gpr1 chr1 63229165 63309823 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146277_Olfr1412 chr1 94484843 94486082 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146305_Olfr420 chr1 176088784 176089871 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146490_Olfr1411 chr1 94493008 94494065 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146491_Olfr1410 chr1 94504416 94505384 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146715_Olfr419 chr1 176180115 176200418 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146716_Olfr432 chr1 175977437 175981444 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146717_Olfr433 chr1 175971174 175973629 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146718_Olfr430 chr1 175999350 176000384 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146720_Olfr421 chr1 176072364 176082596 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146721_Olfr424 chr1 176057388 176067824 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146722_Olfr429 chr1 176019173 176020111 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146761_Olfr414 chr1 176360513 176361670 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146764_Olfr1408 chr1 175060414 175083388 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_146881_Olfr1404 chr1 175145784 175146725 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_147037_Olfr1413 chr1 94469750 94470721 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_148937_Plcd4 chr1 74589462 74614368 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_152895_Kdm5b chr1 136455975 136529487 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_152915_Dner chr1 84366415 84706993 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153064_Ndufs2 chr1 173164989 173180188 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153088_Ctdsp1 chr1 74438065 74443852 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153111_Fev chr1 74915158 74932371 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153114_Otos chr1 94540797 94553072 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153137_Traf3ip3 chr1 195001656 195027877 - chr1 194967560 194967561 34095 60316 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_153154_Tcfap2d chr1 19027377 19157044 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153171_Rgs13 chr1 145985803 146024550 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153179_Pkhd1 chr1 20040166 20661582 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153408_Neurl3 chr1 36321504 36355139 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153502_Ankrd23 chr1 36587038 36593708 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153530_Dis3l2 chr1 88570607 88946671 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153539_Fam5c chr1 148341910 148749599 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153555_Wdr42a chr1 174078166 174127554 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153556_Pms1 chr1 53245508 53353841 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153601_Lgsn chr1 31221394 31261688 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153744_Prkag3 chr1 74785516 74825109 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_153774_Ipo9 chr1 137278207 137330146 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_170597_Creg2 chr1 39677083 39708307 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_170755_Fam134a chr1 75137484 75144869 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172054_Txndc9 chr1 38041434 38054101 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172124_B3gat2 chr1 23755411 23855977 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172294_Sulf1 chr1 12708560 12851249 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172406_Trak2 chr1 58955979 59031177 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172422_Fastkd2 chr1 63777134 63803028 + chr1 63674953 63674954 102180 102180 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_172430_Sphkap chr1 83207585 83404745 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172463_Sned1 chr1 95132418 95197642 + chr1 95196573 95196574 0 64155 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_172484_E030049G20Rik chr1 127810213 128389504 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172485_Thsd7b chr1 131169889 132172070 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172499_Mfsd9 chr1 40828883 40921070 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172510_Mfsd4 chr1 133919383 133964629 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172513_Fam126b chr1 58575029 58643157 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172516_Dstyk chr1 134314046 134363525 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172517_Rbbp5 chr1 134368568 134402423 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172643_Zbtb41 chr1 141318960 141349577 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172644_Dars2 chr1 162970732 163001279 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172647_F11r chr1 173365700 173394971 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172648_Ifi205 chr1 175664572 175958593 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172650_Kctd3 chr1 190794974 190831710 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172652_4632411B12Rik chr1 36381585 36426026 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172653_Slc39a10 chr1 46863572 46949677 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172656_Stradb chr1 59012025 59052817 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172841_Slco5a1 chr1 12857471 12982812 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172843_Tor1aip2 chr1 157906541 157915942 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172844_Fmo9 chr1 168589849 168611976 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172845_Adamts4 chr1 173178880 173192383 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172846_Dnahc14 chr1 183669052 183694102 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172850_Ankmy1 chr1 94757771 94799473 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172851_Cntnap5b chr1 101934704 102382815 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172852_Serpinb13 chr1 108877561 108897772 + chr1 108757655 108757656 119905 119905 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_172853_Cdh7 chr1 111718165 112036714 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_172974_Cops7b chr1 88478926 88503950 + chr1 88419118 88419119 59807 59807 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_173029_Adcy10 chr1 167415324 167506904 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173187_2310035C23Rik chr1 107560448 107651751 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173378_Trp53bp2 chr1 184333536 184392728 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173395_Fam132b chr1 93263007 93270794 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173424_Zbtb37 chr1 162938038 162965197 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173425_Fam124b chr1 80156958 80214611 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173437_Nav1 chr1 137332309 137482282 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173437_Nav1 chr1 137481360 137496527 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173443_Vcpip1 chr1 9709587 9764569 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173760_Hisppd1 chr1 99592475 99667685 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173771_4933406M09Rik chr1 136282517 136287560 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173772_Neu4 chr1 95917070 95928707 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173865_Slc41a1 chr1 133724090 133745438 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173868_St18 chr1 6477297 6885001 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_173870_Mgat4a chr1 37496234 37609425 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_174874_Atg4b chr1 95648097 95687167 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_174985_Gpbar1 chr1 74321873 74326272 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175031_Stk36 chr1 74648039 74683468 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175106_Tmem177 chr1 121793019 121809709 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175118_Dusp28 chr1 94803563 94805012 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175127_Fbxo28 chr1 184242976 184303818 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175170_Pogk chr1 168314763 168391350 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175200_Als2cr11 chr1 59053967 59151744 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175210_Abca12 chr1 71207671 71501632 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175236_Adhfe1 chr1 9538049 9570746 + chr1 9629107 9629108 58361 91058 U NO chr1 9629279 9629280 58533 91230 U NO . . . . . . . . . . . . . .
+NM_175259_Shisa4 chr1 137267654 137274885 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175293_D630023F18Rik chr1 65151863 65176420 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175294_Nucks1 chr1 133807079 133832888 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175296_Mael chr1 168115771 168178081 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175370_Als2cr12 chr1 58714975 58752801 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175382_2700049P18Rik chr1 133344141 133436449 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175439_Mars2 chr1 55294084 55297625 + chr1 55293624 55293625 459 459 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_175443_Etnk2 chr1 135260167 135276893 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175460_Nmnat2 chr1 154802128 154966391 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175461_Fam78b chr1 168898096 169021408 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175564_Tmem169 chr1 72330953 72349677 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175642_Bai3 chr1 25084207 25887514 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_175686_Prrx1 chr1 165175252 165245859 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_176916_Pld5 chr1 177892457 178205403 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_176972_Usp37 chr1 74482084 74590860 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_176980_Ankar chr1 72689581 72747143 - chr1 72779940 72779941 32797 32797 D NO chr1 72780142 72780143 32999 32999 D NO chr1 72825630 72825631 78487 78487 D NO . . . . . . .
+NM_177068_Olfml2b chr1 172569075 172612915 + chr1 172630846 172630847 17931 61771 U NO chr1 172630999 172631000 18084 61924 U NO . . . . . . . . . . . . . .
+NM_177084_Slc9a4 chr1 40636956 40687551 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177129_Cntn2 chr1 134406005 134442705 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177164_A830006F12Rik chr1 70772309 70929065 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177173_A830018L16Rik chr1 11404178 11994163 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177235_Bend6 chr1 33903283 33964764 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177243_Slc26a9 chr1 133640599 133668075 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177305_Arl4c chr1 90569702 90617572 - chr1 90602564 90602565 0 15007 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_177397_Atp6v1g3 chr1 140120875 140186039 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177445_Dars chr1 130260284 130314013 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177587_Aqp12 chr1 94886487 94908846 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177604_AA986860 chr1 132628563 132644539 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177643_Zfp281 chr1 138487073 138526617 + chr1 138447793 138447794 39279 39279 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_177646_Dgkd chr1 89749836 89841946 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177722_6030422M02Rik chr1 9898713 9932156 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177723_Vsig8 chr1 174486069 174513273 + chr1 174386565 174386566 99503 99503 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_177724_D230039L06Rik chr1 180426979 180686112 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177756_Glt25d2 chr1 154223175 154357825 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177757_Kif26b chr1 180720593 180862983 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177781_Trpa1 chr1 14861962 14909072 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177834_Cpa6 chr1 10314801 10710026 - chr1 10627335 10627336 0 82690 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_177838_Fam163a chr1 157923096 158135544 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_177839_Tnn chr1 161966935 162084477 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178051_Mterfd2 chr1 95195779 95202630 - chr1 95196573 95196574 0 6056 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_178055_Dnajb2 chr1 75233016 75242264 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178119_Agap1 chr1 91351421 91791845 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178241_Il8ra chr1 74238380 74241205 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178243_5830403L16Rik chr1 155697272 155747352 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178244_Teddm1 chr1 155724147 155740188 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178399_3110035E14Rik chr1 9591248 9617222 + chr1 9629107 9629108 11885 37859 U NO chr1 9629279 9629280 12057 38031 U NO . . . . . . . . . . . . . .
+NM_178405_Atp1a2 chr1 174201852 174233438 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178593_Rcsd1 chr1 167572007 167639868 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178598_Tagln2 chr1 174430123 174475991 + chr1 174386565 174386566 43557 43557 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_178601_Imp4 chr1 34496377 34511555 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178632_Ints7 chr1 193399085 193447550 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178653_Sccpdh chr1 181598088 181617593 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178690_Rab3gap1 chr1 129765355 129840723 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178691_Yod1 chr1 132612680 132618643 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178692_C130074G19Rik chr1 186695805 186707077 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178775_Rps6kc1 chr1 192524091 192736016 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178779_Rnf152 chr1 107176426 107253513 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178874_Tmcc2 chr1 134252895 134288369 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178883_Gorab chr1 165315039 165340946 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_178884_Obsl1 chr1 75482401 75503218 - chr1 75491987 75491988 0 11230 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_181405_Rnpepl1 chr1 94807467 94817954 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_181546_Syt14 chr1 194713536 194861959 - chr1 194967560 194967561 105601 105601 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_181750_R3hdm1 chr1 129999892 130134312 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_181796_Gstp2 chr1 193897651 193905509 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_182716_Nfasc chr1 134445291 134638354 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_182930_Plekha6 chr1 135077806 135200008 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183019_Arhgef4 chr1 34788954 34873560 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183022_Accn4 chr1 75447063 75470207 + chr1 75491987 75491988 21780 44924 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_183027_Ap1s3 chr1 79591820 79668545 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183028_Pcmtd1 chr1 7079053 7163709 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183124_Defb41 chr1 18241071 18350659 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183355_Pbx1 chr1 170049495 170512777 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_183391_Tnfsf18 chr1 163373523 163524094 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_194333_Slc23a3 chr1 75120731 75130464 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198006_6330578E17Rik chr1 37473934 37474944 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198006_6330578E17Rik chr1 37477057 37486928 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198028_Serpinb10 chr1 109425580 109445838 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198127_Abi2 chr1 60466022 60537998 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198247_Sertad4 chr1 194670313 194693726 - chr1 194655297 194655298 15015 38428 U NO . . . . . . . . . . . . . . . . . . . . .
+NM_198303_Eif5b chr1 38054627 38112414 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198652_6430706D22Rik chr1 90158880 90174174 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198653_Iars2 chr1 187109458 187153280 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198654_Nsl1 chr1 192886918 192919389 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198680_Serpinb3b chr1 109033488 109059720 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198899_Ugcgl1 chr1 36196873 36301555 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_198934_Pou2f1 chr1 167804181 167932753 - chr1 167916419 167916420 0 16333 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_199007_Sgol2 chr1 58026657 58085164 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_199021_Dpp10 chr1 125044486 126749525 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_201363_Serpinb3c chr1 109088051 109198931 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_201376_Serpinb3d chr1 108974770 108980057 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_201641_Ugt1a10 chr1 89922380 90115570 + chr1 89999634 89999635 0 77254 . YES . . . . . . . . . . . . . . . . . . . . .
+NM_206896_Olfr12 chr1 94516341 94538591 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207031_Ano7 chr1 95270385 95302271 + chr1 95196573 95196574 73811 73811 D NO . . . . . . . . . . . . . . . . . . . . .
+NM_207137_Olfr417 chr1 176299050 176299979 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207137_Olfr417 chr1 176321202 176322113 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207158_Olfr427 chr1 176028781 176030538 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207225_Hdac4 chr1 93755950 94103099 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207228_Tsga10 chr1 37783457 37922148 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207233_C1ql2 chr1 122196386 122239751 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207281_4832428D23Rik chr1 44260915 44515719 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207583_Fam5b chr1 160175402 160286644 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207653_Cflar chr1 58768296 58813658 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_207653_Cflar chr1 58813703 58815725 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NM_213616_Atp2b4 chr1 135602265 135697538 - chr1 135592753 135592754 9511 104784 U NO . . . . . . . . . . . . . . . . . . . . .
+NR_002840_Gas5 chr1 162964758 162968663 + . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NR_002858_EG241041 chr1 21268965 21306401 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NR_002870_Dnm3os chr1 164119785 164155671 + chr1 164225779 164225780 70108 105994 U NO . . . . . . . . . . . . . . . . . . . . .
+NR_003623_EG277333 chr1 182251970 182262902 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
+NR_026896_4931440L10Rik chr1 136437533 136449760 - . . . . . . . . . . . . . . . . . . . . . . . . . . . .
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/RnaChipIntegrator/ChangeLog
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/RnaChipIntegrator/ChangeLog Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,250 @@
+2016-02-24 Peter Briggs
+
+ * Version 1.0.0
+ - Complete reimplementation of RnaChipIntegrator to unify internal
+ algorithms, simplify usage and substantially update the
+ documentation.
+ - Installs using 'pip'; can be obtained directly from PyPI using
+ 'pip install RnaChipIntegrator'.
+ - Executable now installs as 'RnaChipIntegrator' (i.e. no '.py'
+ extension)
+ - Documentation now available via ReadTheDocs:
+ http://rnachipintegrator.readthedocs.org/en/latest/
+ - No distinction is now made between 'summits' and 'peaks'; the
+ same algorithm is applied in each case.
+ - The program always finds the nearest genes to each peak, and
+ vice versa. The same distance cutoff and maximum number of hits
+ are applied to both and can be specified using the --cutoff and
+ --number options.
+ - By default all pairs within the cut-off distance are reported
+ unless the user explicitly restricts this to a subset by
+ specifying the --number option (i.e. --number now turned off
+ by default).
+ - By default nearest distances between peaks and gene are
+ calculated from the TSS of the feature to whichever of the peak
+ edges are closer; alternatively distances can be calculated
+ between the nearest pair of peak/gene edges by specifying the
+ --edge=both option.
+ - Any differential expression flags in the input genes file
+ are ignored unless the --only-DE option is specified, in which
+ case only the differentially expressed genes are considered
+ in the analyses.
+ - By default each peak/gene pair is reported on a separate
+ line; the --compact option reports all nearest gene/peaks
+ on a single line of output.
+ - New 'direction' field in output indicates whether hits are
+ up- or downstream from reference.
+ - Specify arbitrary columns from input peaks file using new
+ --peak_cols options to set chromosome, start and end.
+ - Output file names now end with 'gene-centric' and 'peak-centric'.
+ - Excel output is only produced if the --xlsx option is specified;
+ spreadsheets are now output in XLSX format (instead of XLS).
+ - Summary output is only produced if --summary is specified.
+ - The 'rearrange_columns.py' utility has been dropped.
+
+2016-02-18 Peter Briggs
+
+ * Version 0.5.0-alpha.8
+ - Fix typo in XLSX 'notes' sheet.
+
+2016-02-03 Peter Briggs
+
+ * Version 0.5.0-alpha.7
+ - Update --xls option to --xlsx and generate XLSX files
+ (instead of XLS); as XLSX has much greater limits on
+ the number of rows and columns allowed in a worksheet
+ this should address previous problems with having data
+ split over multiple sheets.
+ - Correct headers and placeholders now output when using
+ --compact option when --number is not specified.
+ - Pre-existing output files are explicitly removed before
+ analysis is run (rather than relying on overwrite).
+
+2016-01-29 Peter Briggs
+
+ * Version 0.5.0-alpha.6
+ - Fix broken --xls option (crashed program if specified).
+
+2016-01-29 Peter Briggs
+
+ * Version 0.5.0-alpha.5
+ - Rename 'feature' to 'gene' in program output, documentation etc
+ NB this doesn't affect the program function.
+ - By default all pairs within the cut-off distance are reported
+ unless the user explicitly restricts this to a subset by
+ specifying the --number option (i.e. --number now turned off
+ by default).
+ - Output file names changed to 'feature-centric' and 'peak-centric'.
+ - Options are grouped into subsets when displayed by -h/--help.
+ - Parameter defaults are also given in the documentation.
+ - Peaks in the input have 'start' and 'end' positions which
+ aren't at least 1bp apart cause the program to raise an error.
+
+2015-12-01 Peter Briggs
+
+ * Version 0.5.0-alpha.4
+ - Fix the broken --promoter_region option which was being ignored.
+
+2015-12-20 Peter Briggs
+
+ * Version 0.5.0-alpha.3
+ - --compact now only changes the output format from "multi-line"
+ (i.e. one hit pair per line) to "single-line" (i.e. all hits on
+ the same line). The same fields are reported in both modes.
+ - The explanatory text for the dist_closest field has been updated
+ to make it clearer what this means.
+
+2015-10-28 Peter Briggs
+
+ * Version 0.5.0-alpha.2
+ - Executable now installs as 'RnaChipIntegrator' (i.e. no '.py'
+ extension)
+ - Specify feature type (e.g. 'gene', 'transcript' etc) to be used
+ in output using --feature option.
+ - New 'direction' field in output indicates whether hits are
+ up- or downstream from reference.
+ - Specify arbitrary columns from input peaks file using new
+ --peak_cols options to set chromosome, start and end.
+ - --pad option is automatically implied by the --compact option
+ (i.e. single line output is always padded).
+
+2015-09-01 Peter Briggs
+
+ * Version 0.5.0-alpha.1
+ - Complete reimplementation of RnaChipIntegrator to unify internal
+ algorithms, simplify usage and substantially update the
+ documentation.
+ - No distinction is now made between 'summits' and 'peaks'; the
+ same algorithm is applied in each case.
+ - The program always finds the nearest features to each peak, and
+ vice versa. The same distance cutoff and maximum number of hits
+ are applied to both and can be specified using the --cutoff and
+ --number options.
+ - By default nearest distances between peaks and features are
+ calculated from the TSS of the feature to whichever of the peak
+ edges are closer; alternatively distances can be calculated
+ between the nearest pair of peak/feature edges by specifying the
+ --edge=both option.
+ - Any differential expression flags in the input features file
+ are ignored unless the --only-DE option is specified, in which
+ case only the differentially expressed features are considered
+ in the analyses.
+ - By default each peak/feature pair is reported on a separate
+ line; the --compact option reports all nearest features/peaks
+ on a single line of output.
+ - Excel output is only produced if the --xls option is specified;
+ summary output is only produced if --summary is specified.
+ - The 'rearrange_columns.py' utility has been dropped.
+
+2015-06-10 Peter Briggs
+
+ * Version 0.4.4
+ - Use /usr/bin/env rather than /bin/env to invoke Python interpreter
+ in RnaChipIntegrator.py (was broken for e.g. Ubuntu linux).
+
+2014-05-08 Peter Briggs
+
+ * Version 0.4.3
+ - Update --pad output so that requested number of lines appears for
+ peaks even when there are no hits, and "empty" lines contain the
+ chromosome, start and end positions for the peak in question.
+
+2014-05-02 Peter Briggs
+
+ * Version 0.4.2
+ - Truncate worksheet titles if they exceed maximum length as defined by
+ the spreadsheet writing libraries.
+
+2014-01-20 Peter Briggs
+
+ * Version 0.4.1
+ - Add '--pad' option: for 'NearestTranscriptsToPeakEdge' and
+ 'NearestTSSToPeakEdge' analyses, where necessary adds blank lines to
+ output files and spreadsheet so that each reported peak has the same
+ number of lines associated regardless of the number of hits.
+
+ * Version 0.4.0
+ - Fixed bug in overlap determination, which manifested when a gene was on
+ the negative strand *and* was also wider than the peak. In those cases
+ the start and end of the gene were being assigned incorrectly way around.
+
+ (The bug didn't affect results for other genes on the negative strand
+ which were narrower than the peak.)
+
+ Note that this bug would have a similar effect on determining whether a
+ peak was within the promoter region of a gene on the negative strand.
+ However the lists of nearest genes/peaks were not affected and the results
+ should otherwise have been correct.
+
+2012-02-16 Peter Briggs
+
+ * Version 0.3.3
+ - Added explanatory text to the "notes" page of the output XLS spreadsheet
+ and standardised naming of output files to match XLS page titles.
+ - Minor updates to READMEs/documentation.
+
+2012-01-27 Peter Briggs
+
+ * Version 0.3.2
+ - Output files now use "_vs_" as the default
+ basename (unless overridden by the --project option).
+ - Added example data files in new "examples" directory.
+
+2012-01-20 Peter Briggs
+
+ * Version 0.3.1
+ - Added setup.py into an installable Python package.
+ - Updated documentation.
+
+2012-01-05 Peter Briggs
+
+ * Version 0.3.0
+ - Rename "ID" column to "geneID" (using "ID" has the potential to clash with
+ other programs where this is a reserved word).
+ - Various improvements to some of the column descriptions on the "notes" page
+ of the output XLS file.
+ - In all analyses, now only use those genes flagged as differentially expressed
+ (use all if no flag was specified on the input gene data).
+
+2011-12-19 Peter Briggs
+
+ * Version 0.2.0
+ - Only performs analyses which are appropriate for the supplied ChIP peak
+ data i.e. ignore "region"-based analyses if ChIP data are summits, or
+ summit-based analyses if data are regions.
+
+2011-12-08 Peter Briggs
+
+ * Version 0.1.4
+ - Program will stop if it encounters any 'bad' lines in the RNA-seq/transcipt
+ input data, with the exception of the first line (which is treated as a
+ header and skipped if it contains bad data).
+ - New option --no-xls: suppresses output of XLS spreadsheet.
+
+2011-12-07 Peter Briggs
+
+ * Version 0.1.3
+ - Skip input transcripts where 'start' position is higher than 'end'.
+ - In output spreadsheet, splits the lists of "transcripts inbetween" across
+ multiple columns in the "TSSToSummits" sheet if they exceed 250
+ characters, and creates multiple sheets for result sets that exceed 65536
+ rows.
+
+2011-12-05 Peter Briggs
+
+ * Version 0.1.2
+ - Fixed failure when using with Python 2.4 (optparse.OptionParser "epilog"
+ argument is unsupported)
+
+2011-11-24 Peter Briggs
+
+ * Version 0.1.1
+ - Updated to use optparse library to process command line arguments, and
+ substantially expanded help text (available using -h or --help option).
+
+2011-11-21 Peter Briggs
+
+ * Version 0.1.0
+ - Baseline version of RnaChIPIntegrator.py.
+
+
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/RnaChipIntegrator/INSTALL
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/RnaChipIntegrator/INSTALL Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,57 @@
+Installing RnaChipIntegrator
+============================
+
+Installing the latest version
+*****************************
+
+The recommended method is to install the latest version of the program
+directly from the Python Package Index (PyPI) using::
+
+ pip install RnaChipIntegrator
+
+You may need to have root privileges to install to the system
+directories, in which case preface this command with ``sudo`` i.e.::
+
+ sudo pip install RnaChipIntegrator
+
+Alternatively you can use Python's ``virtualenv`` mechanism to install
+a non-root version (this example creates one under ``.venv``)::
+
+ virtualenv .venv; . .venv/bin/activate
+ pip install RnaChipIntegrator
+
+Installing older versions
+*************************
+
+All versions of the program can be found via:
+
+ * https://github.com/fls-bioinformatics-core/RnaChipIntegrator/releases
+
+To install a specific version of the program download the ``.tar.gz`` or
+``.zip`` file from the above site and install using one of the ``pip``
+recipes above, for example::
+
+ pip install RnaChipIntegrator-0.4.4.tar.gz
+
+Installing directly from GitHub (advanced users/developers)
+***********************************************************
+
+``pip`` can be used to install directly from GitHub::
+
+ pip install git+https://github.com/fls-bioinformatics-core/RnaChipIntegrator
+
+To install a specific version (e.g. ``v0.5.0``)::
+
+ pip install git+https://github.com/fls-bioinformatics-core/RnaChipIntegrator@v0.5.0
+
+To install the ``devel`` branch::
+
+ pip install git+https://github.com/fls-bioinformatics-core/RnaChipIntegrator@devel
+
+Uninstalling RnaChipIntegrator
+==============================
+
+To remove the program do::
+
+ pip uninstall RnaChipIntegrator
+
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/RnaChipIntegrator/LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/RnaChipIntegrator/LICENSE Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,201 @@
+ The Artistic License 2.0
+
+ Copyright (c) 2000-2006, The Perl Foundation.
+
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+Preamble
+
+This license establishes the terms under which a given free software
+Package may be copied, modified, distributed, and/or redistributed.
+The intent is that the Copyright Holder maintains some artistic
+control over the development of that Package while still keeping the
+Package available as open source and free software.
+
+You are always permitted to make arrangements wholly outside of this
+license directly with the Copyright Holder of a given Package. If the
+terms of this license do not permit the full use that you propose to
+make of the Package, you should contact the Copyright Holder and seek
+a different licensing arrangement.
+
+Definitions
+
+ "Copyright Holder" means the individual(s) or organization(s)
+ named in the copyright notice for the entire Package.
+
+ "Contributor" means any party that has contributed code or other
+ material to the Package, in accordance with the Copyright Holder's
+ procedures.
+
+ "You" and "your" means any person who would like to copy,
+ distribute, or modify the Package.
+
+ "Package" means the collection of files distributed by the
+ Copyright Holder, and derivatives of that collection and/or of
+ those files. A given Package may consist of either the Standard
+ Version, or a Modified Version.
+
+ "Distribute" means providing a copy of the Package or making it
+ accessible to anyone else, or in the case of a company or
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+
+ "Distributor Fee" means any fee that you charge for Distributing
+ this Package or providing support for this Package to another
+ party. It does not mean licensing fees.
+
+ "Standard Version" refers to the Package if it has not been
+ modified, or has been modified only in ways explicitly requested
+ by the Copyright Holder.
+
+ "Modified Version" means the Package, if it has been changed, and
+ such changes were not explicitly requested by the Copyright
+ Holder.
+
+ "Original License" means this Artistic License as Distributed with
+ the Standard Version of the Package, in its current version or as
+ it may be modified by The Perl Foundation in the future.
+
+ "Source" form means the source code, documentation source, and
+ configuration files for the Package.
+
+ "Compiled" form means the compiled bytecode, object code, binary,
+ or any other form resulting from mechanical transformation or
+ translation of the Source form.
+
+
+Permission for Use and Modification Without Distribution
+
+(1) You are permitted to use the Standard Version and create and use
+Modified Versions for any purpose without restriction, provided that
+you do not Distribute the Modified Version.
+
+
+Permissions for Redistribution of the Standard Version
+
+(2) You may Distribute verbatim copies of the Source form of the
+Standard Version of this Package in any medium without restriction,
+either gratis or for a Distributor Fee, provided that you duplicate
+all of the original copyright notices and associated disclaimers. At
+your discretion, such verbatim copies may or may not include a
+Compiled form of the Package.
+
+(3) You may apply any bug fixes, portability changes, and other
+modifications made available from the Copyright Holder. The resulting
+Package will still be considered the Standard Version, and as such
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+
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+Distribution of Modified Versions of the Package as Source
+
+(4) You may Distribute your Modified Version as Source (either gratis
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+Modified Version) provided that you clearly document how it differs
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+any non-standard features, executables, or modules, and provided that
+you do at least ONE of the following:
+
+ (a) make the Modified Version available to the Copyright Holder
+ of the Standard Version, under the Original License, so that the
+ Copyright Holder may include your modifications in the Standard
+ Version.
+
+ (b) ensure that installation of your Modified Version does not
+ prevent the user installing or running the Standard Version. In
+ addition, the Modified Version must bear a name that is different
+ from the name of the Standard Version.
+
+ (c) allow anyone who receives a copy of the Modified Version to
+ make the Source form of the Modified Version available to others
+ under
+
+ (i) the Original License or
+
+ (ii) a license that permits the licensee to freely copy,
+ modify and redistribute the Modified Version using the same
+ licensing terms that apply to the copy that the licensee
+ received, and requires that the Source form of the Modified
+ Version, and of any works derived from it, be made freely
+ available in that license fees are prohibited but Distributor
+ Fees are allowed.
+
+
+Distribution of Compiled Forms of the Standard Version
+or Modified Versions without the Source
+
+(5) You may Distribute Compiled forms of the Standard Version without
+the Source, provided that you include complete instructions on how to
+get the Source of the Standard Version. Such instructions must be
+valid at the time of your distribution. If these instructions, at any
+time while you are carrying out such distribution, become invalid, you
+must provide new instructions on demand or cease further distribution.
+If you provide valid instructions or cease distribution within thirty
+days after you become aware that the instructions are invalid, then
+you do not forfeit any of your rights under this license.
+
+(6) You may Distribute a Modified Version in Compiled form without
+the Source, provided that you comply with Section 4 with respect to
+the Source of the Modified Version.
+
+
+Aggregating or Linking the Package
+
+(7) You may aggregate the Package (either the Standard Version or
+Modified Version) with other packages and Distribute the resulting
+aggregation provided that you do not charge a licensing fee for the
+Package. Distributor Fees are permitted, and licensing fees for other
+components in the aggregation are permitted. The terms of this license
+apply to the use and Distribution of the Standard or Modified Versions
+as included in the aggregation.
+
+(8) You are permitted to link Modified and Standard Versions with
+other works, to embed the Package in a larger work of your own, or to
+build stand-alone binary or bytecode versions of applications that
+include the Package, and Distribute the result without restriction,
+provided the result does not expose a direct interface to the Package.
+
+
+Items That are Not Considered Part of a Modified Version
+
+(9) Works (including, but not limited to, modules and scripts) that
+merely extend or make use of the Package, do not, by themselves, cause
+the Package to be a Modified Version. In addition, such works are not
+considered parts of the Package itself, and are not subject to the
+terms of this license.
+
+
+General Provisions
+
+(10) Any use, modification, and distribution of the Standard or
+Modified Versions is governed by this Artistic License. By using,
+modifying or distributing the Package, you accept this license. Do not
+use, modify, or distribute the Package, if you do not accept this
+license.
+
+(11) If your Modified Version has been derived from a Modified
+Version made by someone other than you, you are nevertheless required
+to ensure that your Modified Version complies with the requirements of
+this license.
+
+(12) This license does not grant you the right to use any trademark,
+service mark, tradename, or logo of the Copyright Holder.
+
+(13) This license includes the non-exclusive, worldwide,
+free-of-charge patent license to make, have made, use, offer to sell,
+sell, import and otherwise transfer the Package with respect to any
+patent claims licensable by the Copyright Holder that are necessarily
+infringed by the Package. If you institute patent litigation
+(including a cross-claim or counterclaim) against any party alleging
+that the Package constitutes direct or contributory patent
+infringement, then this Artistic License to you shall terminate on the
+date that such litigation is filed.
+
+(14) Disclaimer of Warranty:
+THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS
+IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED
+WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR
+NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL
+LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF
+ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/RnaChipIntegrator/README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/RnaChipIntegrator/README.rst Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,93 @@
+RnaChipIntegrator: analysis of genes with peak data
+===================================================
+
+.. image:: https://readthedocs.org/projects/rnachipintegrator/badge/?version=latest
+ :target: https://rnachipintegrator.readthedocs.org
+
+.. image:: https://travis-ci.org/fls-bioinformatics-core/RnaChipIntegrator.png?branch=master
+ :target: https://travis-ci.org/fls-bioinformatics-core/RnaChipIntegrator
+
+``RnaChipIntegrator`` is a utility that performs integrated analyses
+of 'gene' data (a set of genes or other genomic features) with 'peak'
+data (a set of regions, for example ChIP peaks) to identify the genes
+nearest to each peak, and vice versa.
+
+The program was originally written specifically for ChIP-Seq and RNA-Seq
+data but works equally well for ChIP-chip and microarray expression data,
+and can also be used to integrate any set of genomic features (e.g.
+canonical genes, CpG islands) with peak data.
+
+Quick Start
+***********
+
+Install the latest version of the program from the Python Package Index
+(PyPI)::
+
+ pip install RnaChipIntegrator
+
+The simplest use of the program is::
+
+ RnaChipIntegrator GENES PEAKS
+
+where ``GENES`` and ``PEAKS`` are tab-delimited files containing the
+'gene' and 'peak' data respectively.
+
+This will output two files with the nearest genes for each peak
+("peak-centric" analysis), and the nearest peaks for each gene
+("gene-centric" analysis).
+
+Full documentation can be found at ReadTheDocs:
+
+ * http://rnachipintegrator.readthedocs.org/en/latest/
+
+See the ``INSTALL`` file for complete installation instructions.
+
+Developers
+**********
+
+The source code for the development version of the program is hosted
+on GitHub in the ``devel`` branch:
+
+ * https://github.com/fls-bioinformatics-core/RnaChipIntegrator/tree/devel
+
+and can be installed directly from GitHub using ``pip``::
+
+ pip install git+https://github.com/fls-bioinformatics-core/RnaChipIntegrator.git@devel
+
+The program depends on the Python ``xlwt``, ``xlrd`` and ``xlutils``
+libraries, which should be installed automatically if using ``pip``.
+
+Documentation based on ``sphinx`` is available under the ``docs`` directory.
+
+To build do either::
+
+ python setup.py sphinx_build
+
+or::
+
+ cd docs
+ make html
+
+both of which create the documentation in the ``docs/_build`` subdirectory.
+
+Running Tests
+*************
+
+The Python unit tests can be run using::
+
+ python setup.py test
+
+Note that this requires the ``nose`` package.
+
+Examples
+********
+
+Example data files can be found in the ``examples`` subdirectory, which
+can be used as input to the program for test or demonstration purposes; see
+the ``README`` file in the same directory for more information.
+
+Licensing
+*********
+
+This software is licensed under the Artistic License 2.0; see the ``LICENSE``
+document.
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/bin/RnaChipIntegrator
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/bin/RnaChipIntegrator Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,10 @@
+#!/home/pjb/virtual-envs/planemo/bin/python
+# EASY-INSTALL-ENTRY-SCRIPT: 'RnaChipIntegrator==1.0.0','console_scripts','RnaChipIntegrator'
+__requires__ = 'RnaChipIntegrator==1.0.0'
+import sys
+from pkg_resources import load_entry_point
+
+if __name__ == '__main__':
+ sys.exit(
+ load_entry_point('RnaChipIntegrator==1.0.0', 'console_scripts', 'RnaChipIntegrator')()
+ )
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/bin/vba_extract.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/bin/vba_extract.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,68 @@
+#!/home/pjb/virtual-envs/planemo/bin/python
+
+##############################################################################
+#
+# vba_extract - A simple utility to extract a vbaProject.bin binary from an
+# Excel 2007+ xlsm file for insertion into an XlsxWriter file.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+import sys
+import shutil
+from zipfile import ZipFile
+from zipfile import BadZipfile
+
+# The VBA project file we want to extract.
+vba_filename = 'vbaProject.bin'
+
+# Get the xlsm file name from the commandline.
+if len(sys.argv) > 1:
+ xlsm_file = sys.argv[1]
+else:
+ print("\nUtility to extract a vbaProject.bin binary from an Excel 2007+ "
+ "xlsm macro file for insertion into an XlsxWriter file."
+ "\n"
+ "See: http://xlsxwriter.readthedocs.org/working_with_macros.html\n"
+ "\n"
+ "Usage: vba_extract file.xlsm\n")
+ exit()
+
+try:
+ # Open the Excel xlsm file as a zip file.
+ xlsm_zip = ZipFile(xlsm_file, 'r')
+
+ # Read the xl/vbaProject.bin file.
+ vba_data = xlsm_zip.read('xl/' + vba_filename)
+
+ # Write the vba data to a local file.
+ vba_file = open(vba_filename, "wb")
+ vba_file.write(vba_data)
+ vba_file.close()
+
+except IOError:
+ # Use exc_info() for Python 2.5+ compatibility.
+ e = sys.exc_info()[1]
+ print("File error: %s" % str(e))
+ exit()
+
+except KeyError:
+ # Usually when there isn't a xl/vbaProject.bin member in the file.
+ e = sys.exc_info()[1]
+ print("File error: %s" % str(e))
+ print("File may not be an Excel xlsm macro file: '%s'" % xlsm_file)
+ exit()
+
+except BadZipfile:
+ # Usually if the file is an xls file and not an xlsm file.
+ e = sys.exc_info()[1]
+ print("File error: %s: '%s'" % (str(e), xlsm_file))
+ print("File may not be an Excel xlsm macro file.")
+ exit()
+
+except:
+ # Catch any other exceptions.
+ e = sys.exc_info()[1]
+ print("File error: %s" % str(e))
+ exit()
+
+print("Extracted: %s" % vba_filename)
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/env.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/env.sh Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,6 @@
+#!/bin/sh
+# Source this to setup rnachipintegrator/1.0.0
+echo Setting up RnaChipIntegrator 1.0.0
+export PATH=/home/pjb/projects/galaxy-tools-update-rnachipintegrator/rnachipintegrator/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/bin:$PATH
+export PYTHONPATH=/home/pjb/projects/galaxy-tools-update-rnachipintegrator/rnachipintegrator/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages:$PYTHONPATH
+#
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/PKG-INFO
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/PKG-INFO Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,22 @@
+Metadata-Version: 1.1
+Name: RnaChipIntegrator
+Version: 1.0.0
+Summary: Analyse genes against peak data, and vice versa
+Home-page: https://github.com/fls-bioinformatics-core/RnaChipIntegrator
+Author: Peter Briggs
+Author-email: peter.briggs@manchester.ac.uk
+License: Artistic License
+Download-URL: https://github.com/fls-bioinformatics-core/RnaChipIntegrator/archive/v1.0.0.tar.gz
+Description: UNKNOWN
+Keywords: RnaChipIntegrator
+Platform: UNKNOWN
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Environment :: Console
+Classifier: License :: OSI Approved :: Artistic License
+Classifier: Operating System :: POSIX
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 2
+Classifier: Programming Language :: Python :: 2.6
+Classifier: Programming Language :: Python :: 2.7
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/SOURCES.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/SOURCES.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,28 @@
+ChangeLog
+INSTALL
+LICENSE
+MANIFEST.in
+README.rst
+setup.cfg
+setup.py
+RnaChipIntegrator.egg-info/PKG-INFO
+RnaChipIntegrator.egg-info/SOURCES.txt
+RnaChipIntegrator.egg-info/dependency_links.txt
+RnaChipIntegrator.egg-info/entry_points.txt
+RnaChipIntegrator.egg-info/not-zip-safe
+RnaChipIntegrator.egg-info/requires.txt
+RnaChipIntegrator.egg-info/top_level.txt
+rnachipintegrator/Features.py
+rnachipintegrator/Peaks.py
+rnachipintegrator/__init__.py
+rnachipintegrator/analysis.py
+rnachipintegrator/cli.py
+rnachipintegrator/distances.py
+rnachipintegrator/output.py
+rnachipintegrator/utils.py
+rnachipintegrator/xls_output.py
+test/test_Features.py
+test/test_Peaks.py
+test/test_analysis.py
+test/test_distances.py
+test/test_output.py
\ No newline at end of file
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/dependency_links.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/dependency_links.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,1 @@
+
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/entry_points.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/entry_points.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,3 @@
+[console_scripts]
+RnaChipIntegrator = rnachipintegrator.cli:main
+
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/installed-files.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/installed-files.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,31 @@
+../rnachipintegrator/Peaks.py
+../rnachipintegrator/xls_output.py
+../rnachipintegrator/distances.py
+../rnachipintegrator/cli.py
+../rnachipintegrator/output.py
+../rnachipintegrator/utils.py
+../rnachipintegrator/analysis.py
+../rnachipintegrator/Features.py
+../rnachipintegrator/__init__.py
+../rnachipintegrator/Peaks.pyc
+../rnachipintegrator/xls_output.pyc
+../rnachipintegrator/distances.pyc
+../rnachipintegrator/cli.pyc
+../rnachipintegrator/output.pyc
+../rnachipintegrator/utils.pyc
+../rnachipintegrator/analysis.pyc
+../rnachipintegrator/Features.pyc
+../rnachipintegrator/__init__.pyc
+../../../../RnaChipIntegrator/README.rst
+../../../../RnaChipIntegrator/LICENSE
+../../../../RnaChipIntegrator/INSTALL
+../../../../RnaChipIntegrator/ChangeLog
+./
+entry_points.txt
+requires.txt
+dependency_links.txt
+PKG-INFO
+top_level.txt
+SOURCES.txt
+not-zip-safe
+../../../../bin/RnaChipIntegrator
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/not-zip-safe
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/not-zip-safe Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,1 @@
+
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/requires.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/requires.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,1 @@
+xlsxwriter >= 0.8.4
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/top_level.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/RnaChipIntegrator-1.0.0-py2.7.egg-info/top_level.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,1 @@
+rnachipintegrator
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/XlsxWriter-0.8.4-py2.7.egg-info/PKG-INFO
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/XlsxWriter-0.8.4-py2.7.egg-info/PKG-INFO Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,87 @@
+Metadata-Version: 1.1
+Name: XlsxWriter
+Version: 0.8.4
+Summary: A Python module for creating Excel XLSX files.
+Home-page: https://github.com/jmcnamara/XlsxWriter
+Author: John McNamara
+Author-email: jmcnamara@cpan.org
+License: BSD
+Description: XlsxWriter
+ ==========
+
+ **XlsxWriter** is a Python module for writing files in the Excel 2007+ XLSX
+ file format.
+
+ XlsxWriter can be used to write text, numbers, formulas and hyperlinks to
+ multiple worksheets and it supports features such as formatting and many more,
+ including:
+
+ * 100% compatible Excel XLSX files.
+ * Full formatting.
+ * Merged cells.
+ * Defined names.
+ * Charts.
+ * Autofilters.
+ * Data validation and drop down lists.
+ * Conditional formatting.
+ * Worksheet PNG/JPEG images.
+ * Rich multi-format strings.
+ * Cell comments.
+ * Integration with Pandas.
+ * Textboxes.
+ * Memory optimization mode for writing large files.
+
+ It supports Python 2.5, 2.6, 2.7, 3.1, 3.2, 3.3, 3.4, 3.5, Jython and PyPy and
+ uses standard libraries only.
+
+ Here is a simple example:
+
+ .. code-block:: python
+
+ import xlsxwriter
+
+
+ # Create an new Excel file and add a worksheet.
+ workbook = xlsxwriter.Workbook('demo.xlsx')
+ worksheet = workbook.add_worksheet()
+
+ # Widen the first column to make the text clearer.
+ worksheet.set_column('A:A', 20)
+
+ # Add a bold format to use to highlight cells.
+ bold = workbook.add_format({'bold': True})
+
+ # Write some simple text.
+ worksheet.write('A1', 'Hello')
+
+ # Text with formatting.
+ worksheet.write('A2', 'World', bold)
+
+ # Write some numbers, with row/column notation.
+ worksheet.write(2, 0, 123)
+ worksheet.write(3, 0, 123.456)
+
+ # Insert an image.
+ worksheet.insert_image('B5', 'logo.png')
+
+ workbook.close()
+
+ .. image:: https://raw.github.com/jmcnamara/XlsxWriter/master/dev/docs/source/_images/demo.png
+
+ See the full documentation at: http://xlsxwriter.readthedocs.org
+
+ Release notes: http://xlsxwriter.readthedocs.org/changes.html
+
+
+Platform: UNKNOWN
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 2.5
+Classifier: Programming Language :: Python :: 2.6
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3.1
+Classifier: Programming Language :: Python :: 3.2
+Classifier: Programming Language :: Python :: 3.3
+Classifier: Programming Language :: Python :: 3.4
+Classifier: Programming Language :: Python :: 3.5
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/XlsxWriter-0.8.4-py2.7.egg-info/SOURCES.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/XlsxWriter-0.8.4-py2.7.egg-info/SOURCES.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,126 @@
+Changes
+LICENSE.txt
+MANIFEST.in
+README.rst
+setup.cfg
+setup.py
+XlsxWriter.egg-info/PKG-INFO
+XlsxWriter.egg-info/SOURCES.txt
+XlsxWriter.egg-info/dependency_links.txt
+XlsxWriter.egg-info/top_level.txt
+docs/readme.html
+docs/_static/basic.css
+docs/_static/default.css
+docs/_static/hello01.png
+docs/_static/logo.png
+docs/_static/pygments.css
+examples/array_formula.py
+examples/autofilter.py
+examples/autofilter_data.txt
+examples/cell_indentation.py
+examples/chart.py
+examples/chart_area.py
+examples/chart_bar.py
+examples/chart_clustered.py
+examples/chart_column.py
+examples/chart_combined.py
+examples/chart_data_table.py
+examples/chart_data_tools.py
+examples/chart_date_axis.py
+examples/chart_doughnut.py
+examples/chart_gradient.py
+examples/chart_line.py
+examples/chart_pareto.py
+examples/chart_pattern.py
+examples/chart_pie.py
+examples/chart_radar.py
+examples/chart_scatter.py
+examples/chart_secondary_axis.py
+examples/chart_stock.py
+examples/chart_styles.py
+examples/chartsheet.py
+examples/comments1.py
+examples/comments2.py
+examples/conditional_format.py
+examples/context_manager.py
+examples/data_validate.py
+examples/datetimes.py
+examples/defined_name.py
+examples/demo.py
+examples/diagonal_border.py
+examples/doc_properties.py
+examples/headers_footers.py
+examples/hello_world.py
+examples/hide_row_col.py
+examples/hide_sheet.py
+examples/http_server_py2.py
+examples/http_server_py3.py
+examples/hyperlink.py
+examples/images.py
+examples/images_bytesio.py
+examples/macros.py
+examples/merge1.py
+examples/merge_rich_string.py
+examples/outline.py
+examples/outline_collapsed.py
+examples/pandas_chart.py
+examples/pandas_chart_columns.py
+examples/pandas_chart_line.py
+examples/pandas_chart_stock.py
+examples/pandas_column_formats.py
+examples/pandas_conditional_format.py
+examples/pandas_datetime.py
+examples/pandas_simple.py
+examples/panes.py
+examples/rich_strings.py
+examples/right_to_left.py
+examples/sparklines1.py
+examples/sparklines2.py
+examples/tab_colors.py
+examples/tables.py
+examples/text_indent.py
+examples/textbox.py
+examples/tutorial1.py
+examples/tutorial2.py
+examples/tutorial3.py
+examples/unicode_polish_utf8.py
+examples/unicode_polish_utf8.txt
+examples/unicode_python2.py
+examples/unicode_python3.py
+examples/unicode_shift_jis.py
+examples/unicode_shift_jis.txt
+examples/vbaProject.bin
+examples/vba_extract.py
+examples/worksheet_protection.py
+xlsxwriter/__init__.py
+xlsxwriter/app.py
+xlsxwriter/chart.py
+xlsxwriter/chart_area.py
+xlsxwriter/chart_bar.py
+xlsxwriter/chart_column.py
+xlsxwriter/chart_doughnut.py
+xlsxwriter/chart_line.py
+xlsxwriter/chart_pie.py
+xlsxwriter/chart_radar.py
+xlsxwriter/chart_scatter.py
+xlsxwriter/chart_stock.py
+xlsxwriter/chartsheet.py
+xlsxwriter/comments.py
+xlsxwriter/compat_collections.py
+xlsxwriter/compatibility.py
+xlsxwriter/contenttypes.py
+xlsxwriter/core.py
+xlsxwriter/drawing.py
+xlsxwriter/format.py
+xlsxwriter/packager.py
+xlsxwriter/relationships.py
+xlsxwriter/shape.py
+xlsxwriter/sharedstrings.py
+xlsxwriter/styles.py
+xlsxwriter/table.py
+xlsxwriter/theme.py
+xlsxwriter/utility.py
+xlsxwriter/vml.py
+xlsxwriter/workbook.py
+xlsxwriter/worksheet.py
+xlsxwriter/xmlwriter.py
\ No newline at end of file
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/XlsxWriter-0.8.4-py2.7.egg-info/dependency_links.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/XlsxWriter-0.8.4-py2.7.egg-info/dependency_links.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,1 @@
+
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/XlsxWriter-0.8.4-py2.7.egg-info/installed-files.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/XlsxWriter-0.8.4-py2.7.egg-info/installed-files.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,70 @@
+../xlsxwriter/__init__.py
+../xlsxwriter/styles.py
+../xlsxwriter/vml.py
+../xlsxwriter/worksheet.py
+../xlsxwriter/chart_bar.py
+../xlsxwriter/format.py
+../xlsxwriter/compatibility.py
+../xlsxwriter/app.py
+../xlsxwriter/packager.py
+../xlsxwriter/chart.py
+../xlsxwriter/chartsheet.py
+../xlsxwriter/compat_collections.py
+../xlsxwriter/relationships.py
+../xlsxwriter/chart_area.py
+../xlsxwriter/chart_scatter.py
+../xlsxwriter/contenttypes.py
+../xlsxwriter/utility.py
+../xlsxwriter/chart_pie.py
+../xlsxwriter/table.py
+../xlsxwriter/sharedstrings.py
+../xlsxwriter/workbook.py
+../xlsxwriter/chart_stock.py
+../xlsxwriter/chart_doughnut.py
+../xlsxwriter/theme.py
+../xlsxwriter/xmlwriter.py
+../xlsxwriter/shape.py
+../xlsxwriter/chart_column.py
+../xlsxwriter/drawing.py
+../xlsxwriter/chart_line.py
+../xlsxwriter/core.py
+../xlsxwriter/chart_radar.py
+../xlsxwriter/comments.py
+../xlsxwriter/__init__.pyc
+../xlsxwriter/styles.pyc
+../xlsxwriter/vml.pyc
+../xlsxwriter/worksheet.pyc
+../xlsxwriter/chart_bar.pyc
+../xlsxwriter/format.pyc
+../xlsxwriter/compatibility.pyc
+../xlsxwriter/app.pyc
+../xlsxwriter/packager.pyc
+../xlsxwriter/chart.pyc
+../xlsxwriter/chartsheet.pyc
+../xlsxwriter/compat_collections.pyc
+../xlsxwriter/relationships.pyc
+../xlsxwriter/chart_area.pyc
+../xlsxwriter/chart_scatter.pyc
+../xlsxwriter/contenttypes.pyc
+../xlsxwriter/utility.pyc
+../xlsxwriter/chart_pie.pyc
+../xlsxwriter/table.pyc
+../xlsxwriter/sharedstrings.pyc
+../xlsxwriter/workbook.pyc
+../xlsxwriter/chart_stock.pyc
+../xlsxwriter/chart_doughnut.pyc
+../xlsxwriter/theme.pyc
+../xlsxwriter/xmlwriter.pyc
+../xlsxwriter/shape.pyc
+../xlsxwriter/chart_column.pyc
+../xlsxwriter/drawing.pyc
+../xlsxwriter/chart_line.pyc
+../xlsxwriter/core.pyc
+../xlsxwriter/chart_radar.pyc
+../xlsxwriter/comments.pyc
+./
+dependency_links.txt
+PKG-INFO
+SOURCES.txt
+top_level.txt
+../../../../bin/vba_extract.py
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/XlsxWriter-0.8.4-py2.7.egg-info/top_level.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/XlsxWriter-0.8.4-py2.7.egg-info/top_level.txt Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,1 @@
+xlsxwriter
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/Features.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/Features.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,492 @@
+#!/bin/env python
+#
+# Features.py: classes for handling feature data
+# Copyright (C) University of Manchester 2011-15 Peter Briggs, Leo Zeef
+# & Ian Donaldson
+#
+"""
+Features.py
+
+Classes for handling feature data.
+
+"""
+
+import logging
+from distances import closestDistanceToRegion
+from utils import make_errline
+
+class FeatureSet:
+ """Class for storing a set of features
+
+ RNA-seq features consists of genes/transcripts/isomers, which
+ are stored individually in Feature objects. This class is a
+ container for a collection of Feature objects and provides
+ methods to operate on the collection, by creating subsets by
+ filtering, and sorting the features based on various criteria.
+
+ """
+ def __init__(self,features_file=None,features_list=None):
+ """Create a new FeatureSet instance
+
+ Raises an exception if there are errors in the input file data
+ (non-numeric fields for start/end positions, end positions
+ occurring before start positions, or illegal strand values).
+
+ Arguments:
+ features_file (str): (optional) the name of an input
+ file to read the feature data from
+ features_list (list): (optional) list of Feature objects
+ to populate the FeatureSet with
+
+ """
+ self.features = []
+ if features_file:
+ self.loadFeaturesFromFile(features_file)
+ elif features_list:
+ for feature in features_list:
+ self.addFeature(feature)
+
+ def loadFeaturesFromFile(self,features_file):
+ """Read features from a file and populate the object
+
+ Arguments:
+ features_file: the name of the input file to read features from.
+
+ """
+ # Local flags etc
+ line_index = 0
+ critical_error = False
+ # Read in data from file
+ fp = open(features_file,'rU')
+ for line in fp:
+ # Increment index
+ line_index += 1
+ # Skip lines starting with #
+ if line.startswith('#'):
+ logging.debug("Feature file: skipped line: %s" % line.strip())
+ continue
+ # Lines are tab-delimited and have at least 5 columns:
+ # ID chr start end strand
+ items = line.strip().split('\t')
+ if len(items) < 5:
+ logging.warning("Feature file: skipped line: %s" % line.strip())
+ logging.warning("Insufficient number of fields (%d)" % \
+ len(items))
+ continue
+ # Check line is valid i.e. start and stop should be
+ # numbers, strand should be + or -
+ problem_fields = []
+ if not items[2].isdigit(): problem_fields.append(2)
+ if not items[3].isdigit(): problem_fields.append(3)
+ if not (items[4] == '+' or items[4] == '-'): problem_fields.append(4)
+ if problem_fields:
+ # If this is the first line then assume it's a header and ignore
+ if line_index == 1:
+ logging.warning("%s: first line ignored as header: %s" %
+ (features_file,line.strip()))
+ else:
+ # Indicate problem field(s)
+ logging.error("%s: critical error line %d: bad values:" %
+ (features_file,line_index))
+ logging.error("%s" % line.strip())
+ logging.error("%s" % make_errline(line.strip(),problem_fields))
+ # This is a critical error: update flag
+ critical_error = True
+ # Continue to next line
+ continue
+ elif int(items[2]) >= int(items[3]):
+ # Start position is same or higher than end
+ logging.error("%s: critical error line %d: 'end' comes before 'start':" %
+ (features_file,line_index))
+ logging.error("%s" % line.strip())
+ logging.error("%s" % make_errline(line.strip(),(2,3)))
+ # This is a critical error: update flag but continue reading
+ critical_error = True
+ continue
+ # Store in a new Feature object
+ feature = Feature(items[0],
+ items[1],
+ items[2],
+ items[3],
+ items[4])
+ # Additional flag
+ if len(items) >= 6:
+ # Is column 6 a flag?
+ try:
+ flag_value = int(items[5])
+ if flag_value != 0 and flag_value != 1:
+ flag_value = None
+ except ValueError:
+ flag_value = None
+ # Store value
+ feature.flag = flag_value
+
+ # Store data
+ self.features.append(feature)
+ fp.close()
+ # Deal with postponed critical errors
+ if critical_error:
+ raise Exception, "critical error(s) in '%s'" % features_file
+ # Return a reference to this object
+ return self
+
+ def addFeature(self,feature):
+ """Append a feature to the FeatureSet object
+
+ Arguments:
+ feature: a Feature instance.
+
+ """
+ self.features.append(feature)
+
+ def filterByChr(self,matchChr):
+ """Return a subset of features filtered by specified chromosome name
+
+ Returns a new FeatureSet object containing only the data from
+ the current object which matches the specified criteria.
+
+ """
+ # Make a new (empty) FeatureSet object
+ feature_subset = FeatureSet()
+ # Populate with only the matching features
+ for feature in self.features:
+ if feature.chrom == matchChr:
+ feature_subset.addFeature(feature)
+ return feature_subset
+
+ def filterByStrand(self,matchStrand):
+ """Return a subset of features filtered by specified strand
+
+ Returns a new FeatureSet object containing only the data from
+ the current object which matches the specified criteria.
+
+ """
+ # Make a new (empty) FeatureSet object
+ feature_subset = FeatureSet()
+ # Populate with only the matching features
+ for feature in self.features:
+ if feature.strand == matchStrand:
+ feature_subset.addFeature(feature)
+ return feature_subset
+
+ def filterByFlag(self,matchFlag):
+ """Return a subset of features filtered by flag value
+
+ Returns a new FeatureSet object containing only the features from
+ the current object which matches the specified criteria.
+
+ Note that if there is no flag (the "isFlagged()" function returns
+ False) then an empty set will be returned.
+
+ """
+ # Make a new (empty) RNASeqData object
+ feature_subset = FeatureSet()
+ # Populate with only the matching features
+ for feature in self.features:
+ if feature.flag == matchFlag:
+ feature_subset.addFeature(feature)
+ return feature_subset
+
+ def filterByTSS(self,limit1,limit2,exclude_limits=False):
+ """Return a subset of features filtered by TSS position
+
+ Returns a new FeatureSet object containing only the features
+ from the current object where the TSS positions fall within a
+ region defined by upper and lower limits.
+
+ limits can be supplied in either order (i.e. highest/lowest
+ or lowest/highest).
+
+ If exclude_limits is False (the default) then TSS positions
+ that fall exactly on one of the boundaries are counted as
+ being within the region; if it is True then these TSS
+ positions will not be considered to lie inside the region.
+
+ """
+ # Sort out upper and lower limits
+ if limit1 > limit2:
+ upper,lower = limit1,limit2
+ else:
+ upper,lower = limit2,limit1
+ # Make a new (empty) FeatureSet object
+ feature_subset = FeatureSet()
+ # Populate with only the matching features
+ for feature in self.features:
+ TSS = feature.getTSS()
+ if exclude_limits:
+ if lower < TSS and TSS < upper:
+ feature_subset.addFeature(feature)
+ else:
+ if lower <= TSS and TSS <= upper:
+ feature_subset.addFeature(feature)
+ return feature_subset
+
+ def sortByDistanceFrom(self,position):
+ """Sort the features into order based on distance from a position
+
+ Sorts the features into order of absolute distance of
+ their TSS to the specified position (closest first).
+
+ Note that this operates on the current object.
+
+ """
+ self.features = sorted(self.features,
+ key=lambda record:
+ abs(record.getTSS()-position))
+ return self
+
+ def sortByClosestEdgeTo(self,position1,position2=None):
+ """Sort the features into order based on closest edge (TSS or TES)
+
+ Sorts the features into order of smallest absolute distance
+ to the specified position (closest first), considering both TSS
+ and TES, using the getClosestEdgeDistanceTo method of the
+ Feature class.
+
+ Note that this operates on the current object.
+
+ """
+ self.features = sorted(self.features,
+ key=lambda record:
+ record.getClosestEdgeDistanceTo(position1,
+ position2))
+ return self
+
+ def sortByClosestTSSTo(self,position1,position2=None):
+ """Sort the features into order based on closest edge to TSS
+
+ Sorts the features into order of smallest absolute distance
+ to the specified position (closest first) to the TSS position,
+ using the getClosestTSSDistanceTo method of the Feature class.
+
+ Note that this operates on the current object.
+
+ """
+ self.features = sorted(self.features,
+ key=lambda record:
+ record.getClosestTSSDistanceTo(position1,
+ position2))
+ return self
+
+ def isFlagged(self):
+ """Check whether feature data includes flags
+
+ Checks whether all the Feature records also have a valid flag
+ associated with them - if yes then returns True (indicating the
+ dataset as a whole is flagged), otherwise returns False.
+
+ """
+ # Check all data and look for any None flags
+ for feature in self.features:
+ if feature.flag is None:
+ return False
+ # All flags valid
+ return True
+
+ def __iter__(self):
+ return iter(self.features)
+
+ def __getitem__(self,key):
+ try:
+ start = key.start
+ stop = key.stop
+ step = key.step
+ slice_ = FeatureSet()
+ for feature in self.features[start:stop:step]:
+ slice_.addFeature(feature)
+ return slice_
+ except AttributeError:
+ return self.features[key]
+
+ def __len__(self):
+ return len(self.features)
+
+ def __eq__(self,other):
+ if len(self) != len(other):
+ return False
+ for f1,f2 in zip(self,other):
+ if f1 != f2:
+ return False
+ return True
+
+ def __ne__(self,other):
+ if len(self) != len(other):
+ return True
+ for f1,f2 in zip(self,other):
+ if f1 != f2:
+ return True
+ return False
+
+class Feature:
+ """Class for storing an 'feature' (gene/transcript/isomer)
+
+ Access the data for the feature using the object's properties:
+
+ id
+ chrom
+ start
+ end
+ strand
+ tss
+ tes
+
+ There are also convenience methods (getTSS, getTES, getPromoterRegion)
+ and methods for calculating various distances.
+
+ """
+ def __init__(self,feature_id,chrom,start,end,strand):
+ self.id = feature_id
+ self.chrom = chrom
+ self.start = int(start)
+ self.end = int(end)
+ self.strand = strand
+ self.flag = None
+ # Set the TSS and TES
+ if self.strand == '+':
+ self.tss = self.start
+ self.tes = self.end
+ elif self.strand == '-':
+ self.tss = self.end
+ self.tes = self.start
+ else:
+ raise Exception("Bad strand: '%s'" % self.strand)
+
+ def __repr__(self):
+ items = [self.id,
+ self.chrom,
+ str(self.start),
+ str(self.end),
+ self.strand]
+ if self.flag != None:
+ items.append(str(self.flag))
+ return '\t'.join(items)
+
+ def __eq__(self,other):
+ return \
+ (self.id == other.id) and \
+ (self.strand == other.strand) and \
+ (self.start == other.start) and \
+ (self.end == other.end)
+
+ def __ne__(self,other):
+ return \
+ (self.id != other.id) or \
+ (self.strand != other.strand) or \
+ (self.start != other.start) or \
+ (self.end != other.end)
+
+ def getTSS(self):
+ """Return the TSS coordinate
+
+ TTS (transcription start site) is the start position for a +ve
+ strand, or end for a -ve strand.
+
+ This is a wrapper for accessing the 'tss' property.
+
+ """
+ return self.tss
+
+ def getTES(self):
+ """Return the TES coordinate
+
+ TES (transcription end site) is the start position for a +ve
+ strand, or end for a -ve strand.
+
+ This is a wrapper for accessing the 'tes' property.
+
+ """
+ return self.tes
+
+ def containsPosition(self,coordinate):
+ """Check whether a coordinate is within the gene coordinates
+
+ Returns True if coordinate lies within start and end, False
+ otherwise.
+
+ """
+ return (self.start <= coordinate and coordinate <= self.end)
+
+ def getClosestTSSDistanceTo(self,position1,position2=None,
+ zero_inside_region=False):
+ """Return distance from TSS to a coordinate or region
+
+ For a single specified position, return the absolute distance
+ between the position and the TSS.
+
+ If a second position is given (specifying a region) then return
+ smallest absolute distance of (TSS,position1) and (TSS,position2).
+
+ By default there is no special treatment when the TSS lies inside
+ the region specified by two positions; to return zero distance in
+ these cases, set the 'zero_inside_region' argument to True.
+
+ """
+ return closestDistanceToRegion(self.getTSS(),
+ position1,position2,
+ zero_inside_region)
+
+ def getClosestTESDistanceTo(self,position1,position2=None,
+ zero_inside_region=False):
+ """Return distance from TES to a coordinate or region
+
+ For a single specified position, return the absolute distance
+ between the position and the TES.
+
+ If a second position is given (specifying a region) then return
+ smallest absolute distance of (TES,position1) and (TES,position2).
+
+ By default there is no special treatment when the TES lies inside
+ the region specified by two positions; to return zero distance in
+ these cases, set the 'zero_inside_region' argument to True.
+
+ """
+ return closestDistanceToRegion(self.getTES(),
+ position1,position2,
+ zero_inside_region)
+
+ def getClosestEdgeDistanceTo(self,position1,position2=None,
+ zero_inside_region=False):
+ """Return closest edge distance to a coordinate or region
+
+ For a single specified position, the closest edge is whichever
+ of the TSS or TES is nearest (smallest absolute distance) from
+ that position i.e. the smallest distance of (TSS,position) and
+ (TES,position).
+
+ If a second position is given (specifying a region) then
+ the closest edge is whichever of the TSS/TES is closest to
+ either position1 or position2 i.e. the smallest distance of
+ (TSS,position1), (TES,position1), (TSS,position2) and
+ (TES,position2).
+
+ By default there is no special treatment when either the TSS
+ or TES lie inside the region specified by two positions; to
+ set this to zero, set the 'zero_inside_region' argument to
+ True.
+
+ """
+ return min(self.getClosestTSSDistanceTo(position1,
+ position2,
+ zero_inside_region),
+ self.getClosestTESDistanceTo(position1,
+ position2,
+ zero_inside_region))
+
+ def getPromoterRegion(self,to_TSS,from_TSS):
+ """Return the coordinates of the promoter region
+
+ The promoter region is a region of coordinates around the
+ TSS of a gene, defined by the supplied distances 'to_TSS'
+ (the distance downstream from the TSS) and 'from_TSS' (the
+ distance upstream from the TSS).
+
+ Returns a tuple containing the start and end coordinates
+ defining the promoter region.
+
+ """
+ if self.strand == '+':
+ return (self.getTSS() - to_TSS,
+ self.getTSS() + from_TSS)
+ else:
+ return (self.getTSS() + to_TSS,
+ self.getTSS() - from_TSS)
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/Features.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/Features.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/Peaks.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/Peaks.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,303 @@
+#!/bin/env python
+#
+# Peaks.py: classes for handling peak data
+# Copyright (C) University of Manchester 2011-16 Peter Briggs, Leo Zeef
+# & Ian Donaldson
+#
+"""
+Peaks.py
+
+Classes for handling peak data
+
+"""
+
+import logging
+from utils import make_errline
+
+class PeakSet:
+ """Class for storing a set of peaks
+
+ ChIP-seq data consists of ChIP peak information, each of which are
+ stored individually in Peak objects. This class is a container for
+ a collection of Peak objects and provides methods to operate on the
+ collection, by creating subsets by filtering, and sorting the data
+ based on various criteria.
+
+ """
+ def __init__(self,peaks_file=None,peaks_list=None,
+ columns=None):
+ """Create a new PeakSet instance
+
+ Arguments:
+ peaks_file (str): (optional) the name of an input file
+ to read the peak data from
+ peaks_list (list): (optional) list of Peak objects to
+ populate the PeakSet with
+ columns (tuple): (optional) tuple with 3 integers
+ indicating which columns to use from the input
+ ``peaks_file`` for the chromosome, start and end
+ columns (if not the first three columns). The
+ columns should be numbered from 1.
+
+ """
+ self.peaks = []
+ if peaks_file:
+ self.loadPeaksFromFile(peaks_file,columns=columns)
+ elif peaks_list:
+ for peak in peaks_list:
+ self.addPeak(peak)
+
+ def loadPeaksFromFile(self,peaks_file,columns=None):
+ """Read peaks data from a file and populate the object
+
+ Arguments:
+ peaks_file (str): the name of the input file to read peaks
+ data from.
+ columns (tuple): (optional) tuple with 3 integers
+ indicating which columns to use from the input
+ ``peaks_file`` for the chromosome, start and end
+ columns (if not the first three columns). The
+ columns should be numbered from 1.
+
+ """
+ # Handle columns
+ if columns is None:
+ columns = (1,2,3)
+ chrom = columns[0] - 1
+ start = columns[1] - 1
+ end = columns[2] - 1
+ ncols = max(chrom,start,end) + 1
+ # Read in from file
+ fp = open(peaks_file,'rU')
+ for line in fp:
+ # Skip lines that start with a # symbol
+ if line.startswith('#'):
+ logging.debug("Peaks file: skipped line: %s" % line.strip())
+ continue
+ # Lines are tab-delimited
+ items = line.strip().split('\t')
+ if len(items) < ncols:
+ logging.warning("Peaks file: skipped line: %s" % line.strip())
+ logging.warning("Insufficient number of fields (%d): need at "
+ "least %d" % (len(items),ncols))
+ continue
+ # Check that items in 'start' and 'end' columns are digits
+ if not items[start].isdigit() or not items[end].isdigit():
+ logging.warning("Peaks file: skipped line: %s" % line.strip())
+ # Indicate problem field(s)
+ bad_fields = []
+ for i in (start,end):
+ if not items[i].isdigit():
+ bad_fields.append(i)
+ logging.warning(" %s" % \
+ make_errline(line,bad_fields))
+ logging.warning("Expected integer at indicated positions")
+ continue
+ # Store in a new Peak object
+ try:
+ peak = Peak(items[chrom],
+ items[start],
+ items[end])
+ except PeakRangeError,ex:
+ logging.error("Peaks file: bad line: %s" % line.strip())
+ logging.error(" %s" %
+ make_errline(line,(start,end)))
+ logging.error("%s" % ex)
+ raise ex
+ self.peaks.append(peak)
+ fp.close()
+ # Return a reference to this object
+ return self
+
+ def addPeak(self,peak):
+ """Append a Peak to the PeakSet object
+
+ Arguments:
+ peak: a Peak instance.
+
+ """
+ self.peaks.append(peak)
+
+ def isSummit(self):
+ """Check whether peak set consists of summits only
+
+ Checks the difference between start and end positions for
+ stored Peak objects - if all differences are equal to 1 then
+ returns True, indicating that the peaks are described as
+ summits; otherwise returns False.
+
+ """
+ for peak in self.peaks:
+ if (peak.end - peak.start) > 1:
+ return False
+ return True
+
+ def filterByChr(self,matchChr):
+ """Return a subset of data filtered by specified chromosome name
+
+ Returns a new PeakSet object containing only the data from
+ the current object which matches the specified criteria.
+
+ """
+ # Make a new (empty) PeakSet object
+ peaks_subset = PeakSet()
+ # Populate with only the matching data lines
+ for peak in self.peaks:
+ if peak.chrom == matchChr:
+ peaks_subset.addPeak(peak)
+ return peaks_subset
+
+ def filterByPosition(self,limit1,limit2,exclude_limits=False):
+ """Return a subset of peaks filtered by position
+
+ Returns a new PeakSet object containing only the data from
+ the current object where the start positions fall within a
+ region defined by upper and lower limits.
+
+ limits can be supplied in either order (i.e. highest/lowest
+ or lowest/highest).
+
+ If exclude_limits is False (the default) then start positions
+ that fall exactly on one of the boundaries are counted as
+ being within the region; if it is True then these start
+ positions will not be considered to lie inside the region.
+
+ """
+ # Sort out upper and lower limits
+ if limit1 > limit2:
+ upper,lower = limit1,limit2
+ else:
+ upper,lower = limit2,limit1
+ # Make a new (empty) PeakSet object
+ peaks_subset = PeakSet()
+ # Populate with only the matching data lines
+ for peak in self.peaks:
+ position = peak.start
+ if exclude_limits:
+ if lower < position and position < upper:
+ peaks_subset.addPeak(peak)
+ else:
+ if lower <= position and position <= upper:
+ peaks_subset.addPeak(peak)
+ return peaks_subset
+
+ def sortByDistanceFrom(self,position):
+ """Sort the peaks into order based on distance from a position
+
+ Sorts the Peak objects into order of absolute distance of
+ their start to the specified position (closest first).
+
+ Note that this operates on the current object.
+
+ """
+ self.peaks = sorted(self.peaks,
+ key=lambda record: min(abs(record.start - position),
+ abs(record.end - position)))
+ return self
+
+ def __iter__(self):
+ return iter(self.peaks)
+
+ def __getitem__(self,key):
+ try:
+ start = key.start
+ stop = key.stop
+ step = key.step
+ slice_ = PeakSet()
+ for peak in self.peaks[start:stop:step]:
+ slice_.addPeak(peak)
+ return slice_
+ except AttributeError:
+ return self.peaks[key]
+
+ def __len__(self):
+ return len(self.peaks)
+
+ def __eq__(self,other):
+ if len(self) != len(other):
+ return False
+ for p1,p2 in zip(self,other):
+ if p1 != p2:
+ return False
+ return True
+
+ def __ne__(self,other):
+ if len(self) != len(other):
+ return True
+ for p1,p2 in zip(self,other):
+ if p1 != p2:
+ return True
+ return False
+
+class Peak:
+ """Class for storing a peak
+
+ Access the data from the line using the object's properties:
+
+ chrom
+ start
+ end
+
+ There are also convenience methods (e.g. insideRegion).
+
+ Raises a PeakRangeError exception if the peak start and end
+ positions don't differ by at least 1bp.
+
+ """
+ def __init__(self,chrom,start,end):
+ self.chrom = chrom.strip('"\'')
+ self.start = int(start)
+ self.end = int(end)
+ if self.start == self.end:
+ raise PeakRangeError("'start' and 'end' positions should "
+ "differ by at least 1bp")
+ elif self.end < self.start:
+ raise PeakRangeError("'end' position must not come before "
+ "'start'")
+
+ def __repr__(self):
+ return "%s\t%s\t%s" % (self.chrom,
+ self.start,
+ self.end)
+
+ def __eq__(self,other):
+ return \
+ (self.chrom == other.chrom) and \
+ (self.start == other.start) and \
+ (self.end == other.end)
+
+ def __ne__(self,other):
+ return \
+ (self.chrom != other.chrom) or \
+ (self.start != other.start) or \
+ (self.end != other.end)
+
+ def insideRegion(self,limit1,limit2,exclude_limits=False):
+ """Check if the peak is contained within a defined region
+
+ The region is defined by upper and lower limits: if the start
+ position lies within these limits then return True, otherwise
+ return false.
+
+ limits can be supplied in either order (i.e. highest/lowest
+ or lowest/highest).
+
+ By default if the start position lies exactly on one of the
+ limits then it is also counted as being within the region;
+ if exclude_limits is set to True then the limits are not
+ considered part of the region.
+
+ """
+ if limit1 > limit2:
+ upper,lower = limit1,limit2
+ else:
+ upper,lower = limit2,limit1
+ if not exclude_limits:
+ return (lower <= self.start and self.start <= upper)
+ else:
+ return (lower < self.start and self.start < upper)
+
+class PeakRangeError(ValueError):
+ """
+ Class for raising errors with peak start/end ranges
+ """
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/Peaks.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/Peaks.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/__init__.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/__init__.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,8 @@
+# Current version of the library
+__version__ = '1.0.0'
+
+def get_version():
+ """Returns a string with the current version of the library (e.g., "0.2.0")
+
+ """
+ return __version__
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/__init__.pyc
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diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/analysis.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/analysis.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,194 @@
+#!/bin/env python
+#
+# analysis.py: analyses of peaks vs features and vice versa
+# Copyright (C) University of Manchester 2011-15 Peter Briggs, Leo Zeef
+# & Ian Donaldson
+#
+"""
+analysis.py
+
+Functions for analysing peaks against features, and vice versa:
+
+- find_nearest_features
+- find_nearest_peaks
+
+"""
+import os
+import logging
+import distances
+from Features import FeatureSet
+from Peaks import PeakSet
+
+#######################################################################
+# Analysis functions
+#######################################################################
+
+# NB there are a few potential optimisations, e.g.:
+# - caching the results of filtering on chromosomes
+# - improving the search over distances e.g. by sorting once on
+# distances from an arbitrary zero, and then calculating distances
+# between things with reference to that?
+
+def find_nearest_features(peaks,features,distance=None,tss_only=False,
+ only_differentially_expressed=False):
+ """
+ Locate nearest features for each peak
+
+ Arguments:
+ features (FeatureList): list of features
+ peaks (PeakList): list of peaks
+ distance (int): optional cut-off distance to apply
+ max_closest (int): optional maximum number of peaks
+ to find per feature
+ tss_only (bool): only consider distances from the
+ feature TSS (default is to consider distances from
+ both the TSS and TES)
+ only_differentially_expressed (bool): only consider
+ features that are flagged as differentially expressed
+ pad (bool): add extra 'None' items to output
+ FeatureSet so that it contains max_closest results
+
+ Yields:
+ tuple: Peak object and a FeatureSet object with the
+ nearest features, for each peak in the input PeakSet
+
+ """
+ # Find nearest features to each peak
+ for peak in peaks:
+ # Only consider features on same chromosome
+ feature_list = features.filterByChr(peak.chrom)
+ # Differentially-expressed features only?
+ if only_differentially_expressed:
+ feature_list = feature_list.filterByFlag(1)
+ if tss_only:
+ sort_features_by_tss_distances(peak,feature_list)
+ else:
+ sort_features_by_edge_distances(peak,feature_list)
+ # Apply distance cut-off
+ if distance is not None:
+ closest = FeatureSet()
+ for feature in feature_list:
+ if tss_only:
+ if distances.distance_tss(peak,feature) > distance:
+ break
+ else:
+ if distances.distance_closest_edge(peak,feature) > distance:
+ break
+ closest.addFeature(feature)
+ feature_list = closest
+ # Return at least one (null) result
+ if not feature_list:
+ feature_list.addFeature(None)
+ # Return result
+ yield (peak,feature_list)
+
+def find_nearest_peaks(features,peaks,distance=None,tss_only=False,
+ only_differentially_expressed=False):
+ """
+ Locate nearest peaks for each feature
+
+ Arguments:
+ features (FeatureList): list of features
+ peaks (PeakList): list of peaks
+ distance (int): optional cut-off distance to apply
+ tss_only (bool): only consider distances from the
+ feature TSS (default is to consider distances from
+ both the TSS and TES)
+ only_differentially_expressed (bool): only consider
+ features that are flagged as differentially expressed
+
+ Yields:
+ tuple: Feature object and a PeakSet object with the
+ nearest peaks, for each feature in the input
+ FeatureSet
+
+ """
+ # Reduce to set of differentially expressed features
+ if only_differentially_expressed:
+ features = features.filterByFlag(1)
+ # Find nearest peaks for each feature
+ for feature in features:
+ # Only consider peaks on same chromosome
+ peak_list = peaks.filterByChr(feature.chrom)
+ # Sort into distance order
+ if tss_only:
+ sort_peaks_by_tss_distances(feature,peak_list)
+ else:
+ sort_peaks_by_edge_distances(feature,peak_list)
+ # Apply distance cut-off
+ if distance is not None:
+ closest = PeakSet()
+ for peak in peak_list:
+ if distances.distance_tss(peak,feature) > distance:
+ break
+ closest.addPeak(peak)
+ peak_list = closest
+ # Return at least one (null) result
+ if not peak_list:
+ peak_list.addPeak(None)
+ # Return results
+ yield (feature,peak_list)
+
+def sort_features_by_edge_distances(peak,features):
+ """
+ Sort features by edge-to-edge distances to a peak
+
+ Arguments:
+ peak (Peak): peak instance
+ features (FeatureSet): set of features that will
+ be sorted into order according to the smallest
+ distance of their edges from the edges of the
+ peak. The sorting is done in place.
+
+ """
+ features.features = sorted(features.features,
+ key = lambda f:
+ distances.edge_distances(peak,f))
+
+def sort_features_by_tss_distances(peak,features):
+ """
+ Sort features by TSS-to-edge distances to a peak
+
+ Arguments:
+ peak (Peak): peak instance
+ features (FeatureSet): set of features that will
+ be sorted into order according to the smallest
+ distance of their TSS positions to the edges of
+ the peak. The sorting is done in place.
+
+ """
+ features.features = sorted(features.features,
+ key = lambda f:
+ distances.tss_distances(peak,f))
+
+def sort_peaks_by_edge_distances(feature,peaks):
+ """
+ Sort peaks by edge-to-edge distances to a feature
+
+ Arguments:
+ feature (Feature): feature instance
+ peaks (PeakSet): set of peaks that will be
+ sorted into order according to the smallest
+ distance of their edges from the edges of the
+ feature. The sorting is done in place.
+
+ """
+ peaks.peaks = sorted(peaks.peaks,
+ key = lambda p:
+ distances.edge_distances(p,feature))
+
+def sort_peaks_by_tss_distances(feature,peaks):
+ """
+ Sort peaks by edge-to-TSS distances to a feature
+
+ Arguments:
+ feature (Feature): feature instance
+ peaks (PeakSet): set of peaks that will be
+ sorted into order according to the smallest
+ distance of their edges from the TSS position
+ of the feature. The sorting is done in place.
+
+ """
+ peaks.peaks = sorted(peaks.peaks,
+ key = lambda p:
+ distances.tss_distances(p,feature))
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/analysis.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/analysis.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/cli.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/cli.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,410 @@
+#!/usr/bin/env python
+#
+# RnaChipIntegrator.py: analyse genomic features (genes) with peak data
+# Copyright (C) University of Manchester 2011-16 Peter Briggs, Leo Zeef
+# & Ian Donaldson
+#
+# This code is free software; you can redistribute it and/or modify it
+# under the terms of the Artistic License 2.0 (see the file LICENSE
+# included with the distribution).
+#
+########################################################################
+#
+# RnaChipIntegrator.py
+#
+#########################################################################
+
+"""
+RnaChipIntegrator.py
+
+Analyse genomic features (genes) with peak data.
+
+"""
+
+#######################################################################
+# Imports
+#######################################################################
+
+import sys
+import os
+import optparse
+import time,datetime
+from .Features import FeatureSet
+from .Peaks import PeakSet
+import analysis
+import output
+import xls_output
+import logging
+logging.getLogger().setLevel(logging.WARNING)
+logging.basicConfig(format='%(levelname)s: %(message)s')
+
+from . import get_version
+__version__ = get_version()
+
+DEFAULT_FEATURE_TYPE = 'gene'
+
+#######################################################################
+# Main program
+#######################################################################
+
+def main(args=None):
+ """
+ Implements the 'RnaChipIntegrator' CLI
+
+ """
+
+ # Command line arguments
+ if args is None:
+ args = sys.argv[1:]
+
+ # Defaults
+ promoter = (1000,100)
+ max_distance = 1000000
+
+ # Parse command line
+ p = optparse.OptionParser(usage="%prog [options] GENES PEAKS",
+ version="%prog "+__version__,
+ description=
+ "Analyse GENES (any set of genes or genomic "
+ "features) against PEAKS (a set of regions) "
+ "and report nearest genes to each peak (and "
+ "vice versa)")
+
+ # Analysis options
+ analysis_opts = optparse.OptionGroup(p,"Analysis options")
+ analysis_opts.add_option('--cutoff',action='store',dest='max_distance',
+ type='int',default=max_distance,
+ help="Maximum distance allowed between peaks "
+ "and genes before being omitted from the "
+ "analyses (default %dbp; set to zero for no "
+ "cutoff)" % max_distance)
+ analysis_opts.add_option('--edge',action='store',dest="edge",
+ type="choice",choices=('tss','both'),
+ default='tss',
+ help="Gene edges to consider when calculating "
+ "distances between genes and peaks, either: "
+ "'tss' (default: only use gene TSS) or 'both' "
+ "(use whichever of TSS or TES gives shortest "
+ "distance)")
+ analysis_opts.add_option('--only-DE',action='store_true',
+ dest='only_diff_expressed',default=False,
+ help="Only use genes flagged as differentially "
+ "expressed in analyses (input gene data must "
+ "include DE flags)")
+ p.add_option_group(analysis_opts)
+
+ # Reporting options
+ reporting_opts = optparse.OptionGroup(p,"Reporting options")
+ reporting_opts.add_option('--number',action='store',dest='max_closest',
+ type='int',default=None,
+ help="Filter results after applying --cutoff "
+ "to report only the nearest MAX_CLOSEST number "
+ "of pairs for each gene/peak from the analyses "
+ "(default is to report all results)")
+ reporting_opts.add_option('--promoter_region',action="store",
+ dest="promoter_region",
+ default="%d,%d" % promoter,
+ help="Define promoter region with respect to "
+ "gene TSS in the form UPSTREAM,DOWNSTREAM "
+ "(default -%d to %dbp of TSS)" % promoter)
+ p.add_option_group(reporting_opts)
+
+ # Output options
+ output_opts = optparse.OptionGroup(p,"Output options")
+ output_opts.add_option('--name',action='store',dest='name',default=None,
+ help="Set basename for output files")
+ output_opts.add_option('--compact',action='store_true',dest='compact',
+ default=False,
+ help="Output all hits for each peak or gene on a "
+ "single line (cannot be used with --summary)")
+ output_opts.add_option('--summary',action='store_true',dest='summary',
+ default=False,
+ help="Output 'summary' for each analysis, "
+ "consisting of only the top hit for each peak or "
+ "gene (cannot be used with --compact)")
+ output_opts.add_option('--pad',action="store_true",dest="pad_output",
+ help="Where less than MAX_CLOSEST hits are found, "
+ "pad output with blanks to ensure that MAX_CLOSEST "
+ "hits are still reported (nb --pad is implied for "
+ "--compact)")
+ output_opts.add_option('--xlsx',action="store_true",dest="xlsx_output",
+ help="Output XLSX spreadsheet with results")
+ p.add_option_group(output_opts)
+
+ # Advanced options
+ advanced_opts = optparse.OptionGroup(p,"Advanced options")
+ advanced_opts.add_option('--feature',action="store",dest="feature_type",
+ help="rename '%s' to FEATURE_TYPE in output (e.g. "
+ "'transcript' etc)" % DEFAULT_FEATURE_TYPE)
+ advanced_opts.add_option('--peak_cols',action="store",dest="peak_cols",
+ help="list of 3 column indices (e.g. '1,4,5') "
+ "indicating columns to use for chromosome, "
+ "start and end from the input peak file (if not "
+ "first three columns).")
+ p.add_option_group(advanced_opts)
+
+ # Process command line
+ options,args = p.parse_args()
+
+ # Input files
+ if len(args) != 2:
+ p.error("need to supply 2 files (genes and peaks)")
+ gene_file,peak_file = args
+
+ # Report version and authors
+ p.print_version()
+ print
+ print "Find nearest peaks to genes (and vice versa)"
+ print
+ print "University of Manchester"
+ print "Faculty of Life Sciences"
+ print "Bioinformatics Core Facility"
+ print "Authors: Peter Briggs, Ian Donaldson and Leo Zeef"
+ print
+ print "If you use this program in your published work then please cite:"
+ print
+ print " Briggs PJ, Donaldson IJ, Zeef LAH. RnaChipIntegrator"
+ print " (version %s). Available at:" % __version__
+ print " https://github.com/fls-bioinformatics-core/RnaChipIntegrator"
+ print
+
+ # Promoter region
+ promoter = (abs(int(options.promoter_region.split(',')[0])),
+ abs(int(options.promoter_region.split(',')[1])))
+
+ # Reporting options
+ max_distance = options.max_distance
+ if max_distance <= 0:
+ max_distance = None
+ max_closest = options.max_closest
+
+ # Gene edge to use
+ if options.edge == 'tss':
+ tss_only = True
+ else:
+ tss_only = False
+
+ # Reporting formats
+ if options.compact:
+ mode = output.SINGLE_LINE
+ peak_fields = ('peak.chr','peak.start','peak.end',
+ 'list(feature.id,strand,TSS,TES,dist_closest,'
+ 'dist_TSS,dist_TES,direction,overlap_feature,'
+ 'overlap_promoter)')
+ gene_fields = ('feature.id','feature.chr','feature.start',
+ 'feature.end','feature.strand',
+ 'list(chr,start,end,dist_closest,dist_TSS,'
+ 'direction,in_the_feature)')
+ placeholder = '.'
+ if options.summary:
+ options.summary = False
+ logging.error("--summary option not compatible with --compact")
+ sys.exit(1)
+ else:
+ mode = output.MULTI_LINE
+ peak_fields = ('peak.chr','peak.start','peak.end',
+ 'feature.id','strand','TSS','TES',
+ 'dist_closest','dist_TSS','dist_TES',
+ 'direction','overlap_feature','overlap_promoter')
+ gene_fields = ('feature.id','feature.chr','feature.start',
+ 'feature.end','feature.strand',
+ 'chr','start','end','dist_closest','dist_TSS',
+ 'direction','in_the_feature')
+ placeholder = '---'
+
+ # Feature type
+ if options.feature_type is None:
+ feature_type = 'gene'
+ else:
+ feature_type = options.feature_type
+
+ # Columns to extract from input peaks file
+ if options.peak_cols is None:
+ peak_cols = (1,2,3)
+ else:
+ try:
+ peak_cols = tuple([int(x)
+ for x in options.peak_cols.split(',')])
+ except Exception, ex:
+ p.error("Bad column assignment for --peak_cols")
+
+ # Report settings
+ print "Input genes file: %s" % gene_file
+ print "Input peaks file: %s" % peak_file
+ print
+ print "Maximum cutoff distance: %d (bp)" % max_distance
+ print "Maximum no. of hits : %s" % ('All' if max_closest is None
+ else "%d" % max_closest)
+ print "Promoter region : -%d to %d (bp from TSS)" % promoter
+ print
+ if tss_only:
+ print "Distances will be calculated from gene TSS only"
+ else:
+ print "Distances will be calculated from nearest of gene TSS or TES"
+ print
+ print "Genomic features are '%ss'" % feature_type
+ print
+
+ # Read in gene data
+ try:
+ genes = FeatureSet(gene_file)
+ except Exception, ex:
+ logging.critical("Failed to read in gene data: %s" % ex)
+ print "Please fix errors in input file before running again"
+ sys.exit(1)
+ if not len(genes):
+ logging.error("No gene data read in")
+ sys.exit(1)
+ print "%d gene records read in" % len(genes)
+
+ # Differential expression handling
+ use_differentially_expressed = False
+ if genes.isFlagged():
+ print "\tGene data include differential expression flag"
+ print "\t%d genes flagged as differentially expressed" % \
+ len(genes.filterByFlag(1))
+ if options.only_diff_expressed:
+ print
+ print "*** Only differentially expressed genes will used ***"
+ use_differentially_expressed = True
+ elif options.only_diff_expressed:
+ logging.error("--only-DE flag needs input genes flagged as "
+ "differentially expressed")
+ sys.exit(1)
+ print
+
+ # Read in peak data
+ print "Using columns %s from peaks file as chrom, start, end" % \
+ (peak_cols,)
+ try:
+ peaks = PeakSet(peak_file,columns=peak_cols)
+ except Exception,ex:
+ logging.critical("Failed to read peak data (%s)" % ex)
+ print "Please fix errors in input file before running again"
+ sys.exit(1)
+ if not len(peaks):
+ logging.error("No peak data read in")
+ sys.exit(1)
+ print "%d peak records read in" % len(peaks)
+ if peaks.isSummit():
+ print "\tPeak data are summits"
+ else:
+ print "\tPeak data are regions"
+ print
+
+ # Set up output files
+ if options.name is not None:
+ basename = options.name
+ else:
+ basename = os.path.splitext(os.path.basename(gene_file))[0]
+ peak_centric_out = basename+"_peak_centric.txt"
+ gene_centric_out = basename+"_gene_centric.txt"
+ if options.summary:
+ peak_centric_summary = basename+"_peak_centric_summary.txt"
+ gene_centric_summary = basename+"_gene_centric_summary.txt"
+ else:
+ peak_centric_summary = None
+ gene_centric_summary = None
+ if options.xlsx_output:
+ xlsx_out = basename+".xlsx"
+ else:
+ xlsx_out = None
+
+ # Clean up any pre-existing output files that would otherwise
+ # be overwritten
+ print "Checking for pre-existing output files"
+ for f in (peak_centric_out,peak_centric_summary,
+ gene_centric_out,gene_centric_summary,
+ xlsx_out):
+ if f is not None and os.path.isfile(f):
+ print "\tRemoving %s" % f
+ os.remove(f)
+ print
+
+ # Do the analyses
+ print "**** Peak-centric analysis: nearest genes to each peak ****"
+ reporter = output.AnalysisReportWriter(mode,peak_fields,
+ promoter_region=promoter,
+ null_placeholder=placeholder,
+ max_hits=max_closest,
+ pad=options.pad_output,
+ outfile=peak_centric_out,
+ summary=peak_centric_summary,
+ feature_type=feature_type)
+ for peak,nearest_genes in analysis.find_nearest_features(
+ peaks,genes,tss_only=tss_only,distance=max_distance,
+ only_differentially_expressed=use_differentially_expressed):
+ reporter.write_nearest_features(peak,nearest_genes)
+ reporter.close()
+ print "Results written to %s" % peak_centric_out
+ if peak_centric_summary:
+ print "Summary written to %s" % peak_centric_summary
+ print
+
+ print "**** Gene-centric analysis: nearest peaks to each gene ****"
+ reporter = output.AnalysisReportWriter(mode,gene_fields,
+ null_placeholder=placeholder,
+ max_hits=max_closest,
+ pad=options.pad_output,
+ outfile=gene_centric_out,
+ summary=gene_centric_summary,
+ feature_type=feature_type)
+ for gene,nearest_peaks in analysis.find_nearest_peaks(
+ genes,peaks,tss_only=tss_only,distance=max_distance,
+ only_differentially_expressed=use_differentially_expressed):
+ reporter.write_nearest_peaks(gene,nearest_peaks)
+ reporter.close()
+ print "Results written to %s" % gene_centric_out
+ if gene_centric_summary:
+ print "Summary written to %s" % gene_centric_summary
+ print
+
+ # Make XLSX file
+ if options.xlsx_output:
+ print "**** Writing XLSX file ****"
+ xlsx = xls_output.XLSX(xlsx_out,p.get_version(),feature_type)
+ # Write the settings
+ xlsx.append_to_notes("Input %ss file\t%s" % (feature_type,
+ gene_file))
+ xlsx.append_to_notes("Input peaks file\t%s" % peak_file)
+ xlsx.append_to_notes("Maximum cutoff distance (bp)\t%d" % max_distance)
+ xlsx.append_to_notes("Maximum no. of hits to report\t%s"
+ % ('All' if max_closest is None
+ else "%d" % max_closest))
+ xlsx.append_to_notes("Promoter region (bp from TSS)\t-%d to %d" %
+ promoter)
+ if tss_only:
+ xlsx.append_to_notes("Distances calculated from\tTSS only")
+ else:
+ xlsx.append_to_notes("Distances calculated from\tTSS or TES")
+ xlsx.append_to_notes("Only use differentially expressed %ss\t%s" %
+ (feature_type,
+ "Yes" if use_differentially_expressed else "No"))
+ # Add features to peaks
+ xlsx.write_peak_centric(peak_fields)
+ xlsx.add_result_sheet('Peak-centric',peak_centric_out)
+ if options.summary:
+ xlsx.append_to_notes("\n'Peak-centric (summary)' lists the 'top' "
+ "result (i.e. closest peak/%s pair) for each "
+ "peak" % feature_type)
+ xlsx.add_result_sheet('Peak-centric (summary)',
+ peak_centric_summary)
+ # Add peaks to features
+ xlsx.write_feature_centric(gene_fields)
+ xlsx.add_result_sheet('%s-centric' % feature_type.title(),
+ gene_centric_out)
+ if options.summary:
+ xlsx.append_to_notes("\n'%s-centric (summary)' lists the 'top' "
+ "result (i.e. closest %s/peak pair) for each "
+ "%s" % (feature_type.title(),
+ feature_type,
+ feature_type))
+ xlsx.add_result_sheet('%s-centric (summary)' %
+ feature_type.title(),
+ gene_centric_summary)
+ xlsx.write()
+ print "Wrote %s" % xlsx_out
+ print
+
+ # Finished
+ print "Done"
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/cli.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/cli.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/distances.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/distances.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,347 @@
+#!/bin/env python
+#
+# distances.py: functions for determining distances and overlaps
+# Copyright (C) University of Manchester 2011-15 Peter Briggs, Leo Zeef
+# & Ian Donaldson
+#
+"""
+distances.py
+
+Functions for determining distances and overlaps:
+
+- closestDistanceToRegion: distance from a reference position to a
+ coordinate or region
+- regions_overlap: determine if two regions have any overlap
+- GetNearestTranscriptToPeak: compare two transcripts against the same
+ region
+- direction: indicate whether two regions are upstream,
+ downstream, or overlapping
+
+Also defines constants:
+
+- UPSTREAM
+- DOWNSTREAM
+- OVERLAP
+
+"""
+# Module constants (used for 'direction' function)
+UPSTREAM = -1
+DOWNSTREAM = 1
+OVERLAP = 0
+
+def closestDistanceToRegion(reference,position1,position2=None,
+ zero_inside_region=False):
+ """Return distance from a reference position to a coordinate or region
+
+ For a single specified position, return the absolute distance between
+ that position and the reference point.
+
+ If a second position is given (specifying a region) then return the
+ smallest absolute distance of (reference,position1) and
+ (reference,position2).
+
+ By default there is no special treatment when the reference lies inside
+ the region specified by two positions; to return zero distance in
+ these cases, set the 'zero_inside_region' argument to True.
+ """
+ # Only one position given
+ if position2 is None:
+ return abs(reference - position1)
+ # Is point inside specified region?
+ if zero_inside_region:
+ if position1 < position2:
+ upper,lower = position2,position1
+ else:
+ upper,lower = position1,position2
+ if (lower < reference and reference < upper):
+ return 0
+ # Outside specified region - return absolute distance
+ return min(abs(reference - position1),abs(reference - position2))
+
+def regions_overlap(region1,region2):
+ """Determine if two regions have any overlap
+
+ Returns True if any part of the first region overlaps any part of
+ the second region (including one region being completely inside the
+ other).
+
+ Arguments:
+ region1: tuple of numbers representing the limits of the first
+ region, can be in any order e.g. (0,10) or (10,0)
+ region2: tuple of numbers representing the limits of the second
+ region.
+
+ Returns:
+ True if there is overlap, False otherwise.
+ """
+ # Widest region
+ if (abs(region1[0] - region1[1]) > abs(region2[0] - region2[1])):
+ wide,narrow = region1,region2
+ else:
+ wide,narrow = region2,region1
+ # Determine upper/lower limits of region #1
+ if wide[0] < wide[1]:
+ lower,upper = wide[0],wide[1]
+ else:
+ lower,upper = wide[1],wide[0]
+ # Regions overlap if either start or end of region #2 lies
+ # within region #1 (or vice versa)
+ return ((lower <= narrow[0] and narrow[0] <= upper) or
+ (lower <= narrow[1] and narrow[1] <= upper))
+
+def GetNearestTranscriptToPeak(rna_data1,rna_data2,chip_peak):
+ """Compare two RNA-seq transcripts against the same ChIP-seq peak.
+
+ Given two RNASeqDataLine objects (one for each of the transcripts)
+ and a ChIPSeqDataLine object (for the ChIP peak), return the
+ transcript which lies closest (regardless of direction) to the ChIP
+ peak.
+
+ Note: if the two transcripts are equidistant from the ChIP peak
+ then return the first one.
+ """
+
+ # Check that one or both are defined
+ if not rna_data1:
+ return rna_data2
+ elif not rna_data2:
+ return rna_data1
+
+ # Get the distances from the peak
+ distance1 = rna_data1.getTSS() - chip_peak.start
+ distance2 = rna_data2.getTSS() - chip_peak.start
+
+ # See which is closest
+ dist_diff = abs(distance2) - abs(distance1)
+ if dist_diff < 0:
+ # Transcript 2 is nearest
+ return rna_data2
+ else:
+ # Transcript 1 is nearest
+ return rna_data1
+
+def edge_distances(peak,feature):
+ """
+ Return distances between peak and feature edges
+
+ Arguments:
+ peak (Peak): peak instance
+ feature (Feature): feature instance
+
+ Returns:
+ tuple: a pair of distances, the first being the
+ smallest distance between an edge of the peak
+ region and an edge of the feature region and
+ the second being the distance from the same peak
+ edge to the opposite feature edge.
+ Both distances are zero if the peak is entirely
+ contained within the feature (or vice versa).
+ If there is partial overlap then the smallest
+ distance is returned as zero, the second is
+ the amount of the peak that lies outside the
+ feature.
+
+ """
+ if ((peak.start >= feature.start and
+ peak.end <= feature.end) or
+ (feature.start >= peak.start and
+ feature.end <= peak.end)):
+ # Peak entirely contained in feature (or vice versa)
+ return (0,0)
+ # All possible distances
+ ds_fs = abs(peak.start - feature.start)
+ ds_fe = abs(peak.start - feature.end)
+ de_fs = abs(peak.end - feature.start)
+ de_fe = abs(peak.end - feature.end)
+ if peak.start >= feature.start and peak.start <= feature.end:
+ # Peak start inside feature:
+ #
+ # | PPPPPPP |
+ # |--------FFFFFFFFF---------|
+ #
+ # Return distances from peak end to feature end
+ return (0,de_fe)
+ if peak.end >= feature.start and peak.end <= feature.end:
+ # Peak end inside feature
+ #
+ # | PPPPPPP |
+ # |--------FFFFFFFFF---------|
+ #
+ # Return distances from peak start to feature start
+ return (0,ds_fs)
+ if ds_fe < de_fs:
+ # No overlap: peak start to feature end is smallest
+ #
+ # | PPPPPPP |
+ # |----FFFFFFFFF--------------|
+ #
+ return (ds_fe,ds_fs)
+ else:
+ # No overlap: peak end to feature start is smallest
+ #
+ # | PPPPPPP |
+ # |-------------FFFFFFFFF-----|
+ #
+ return (de_fs,de_fe)
+
+def tss_distances(peak,feature):
+ """
+ Return distances between peak edges and feature TSS
+
+ Arguments:
+ peak (Peak): peak instance
+ feature (Feature): feature instance
+
+ Returns:
+ tuple: a pair of distances, the first being the
+ smallest distance between an edge of the peak
+ region to the TSS of the feature region, and
+ the second being the distance from the other peak
+ edge to the TSS.
+ If the TSS position is entirely contained within
+ the peak then the smallest distance is returned as
+ zero, the second is the average of the distances
+ to the two peak edges from the TSS.
+
+ """
+ # TSS is considered as a point
+ if (feature.tss >= peak.start and
+ feature.tss <= peak.end):
+ # TSS entirely contained in the peak
+ # Rank using the average distance of the peak
+ # edges from the TSS
+ return (0,(abs(feature.tss - peak.start) +
+ abs(feature.tss - peak.end))/2)
+ # Possible distances to TSS
+ d_tss = [abs(feature.tss - peak.start),
+ abs(feature.tss - peak.end)]
+ d_tss.sort()
+ return tuple(d_tss)
+
+def distance_closest_edge(peak,feature):
+ """
+ Get distance from a peak to a feature
+
+ Arguments:
+ peak (Peak): peak
+ feature (Feature): feature
+
+ Returns:
+ int: Smallest absolute distance from the peak to
+ the feature.
+
+ """
+ return min(closestDistanceToRegion(peak.start,
+ feature.tss,feature.tes,
+ zero_inside_region=True),
+ closestDistanceToRegion(peak.end,
+ feature.tss,feature.tes,
+ zero_inside_region=True))
+
+def distance_tss(peak,feature):
+ """
+ Get distance from a peak to a feature TSS
+
+ Arguments:
+ peak (Peak): peak
+ feature (Feature): feature
+
+ Returns:
+ int: Smallest absolute distance from the peak to
+ the feature TSS.
+
+ """
+ return closestDistanceToRegion(feature.tss,
+ peak.start,peak.end,
+ zero_inside_region=True)
+
+def distance_tes(peak,feature):
+ """
+ Get distance from a peak to a feature TES
+
+ Arguments:
+ peak (Peak): peak
+ feature (Feature): feature
+
+ Returns:
+ int: Smallest absolute distance from the peak to
+ the feature TES.
+
+ """
+ return closestDistanceToRegion(feature.tes,
+ peak.start,peak.end,
+ zero_inside_region=True)
+
+def direction(region1,region2,strand=None):
+ """
+ Direction (up- or downstream) of one region relative to another
+
+ Given two regions (either Peak or Feature instances),
+ determine the direction of the second region relative to
+ the first.
+
+ For positive strand, 'upstream' means that the test region
+ occurs "before" the reference (i.e. has smaller coordinate
+ positions), 'downstream' indicates it occurs after. For the
+ negative strand the meaning is reversed.
+
+ If region1 partially overlaps region2 then the upstream or
+ downstream position will still be determined. However if
+ one region wholly overlaps the other then 'overlap' will
+ be returned instead.
+
+ Arguments:
+ region1 (Peak/Feature): reference region
+ region2 (Peak/Feature): region to get direction of
+ relative to region1
+ strand (str): (optional) explicit strand direction
+ ('+' or '-').
+
+ Returns:
+ int: UPSTREAM, DOWNSTREAM or OVERLAP (module constants)
+ indicating direction of test region relative to
+ reference region.
+
+ """
+ # Get strandedness info
+ if strand is None:
+ try:
+ strand = region1.strand
+ except AttributeError:
+ try:
+ strand = region2.strand
+ except AttributeError:
+ strand = '+'
+ # Check for overlapping regions
+ if (region1.start >= region2.start and region1.end <= region2.end) or \
+ (region2.start >= region1.start and region2.end <= region1.end):
+ return OVERLAP
+ if region2.start >= region1.start and region2.start <= region1.end:
+ # region2 start inside feature:
+ #
+ # | 2222222 |
+ # |--------111111111---------|
+ #
+ # Return distances from peak end to feature end
+ return (DOWNSTREAM if strand == '+' else UPSTREAM)
+ if region2.end >= region1.start and region2.end <= region1.end:
+ # region2 end inside region1
+ #
+ # | 2222222 |
+ # |--------111111111---------|
+ #
+ return (UPSTREAM if strand == '+' else DOWNSTREAM)
+ if region1.end < region2.start:
+ # No overlap: peak start to feature end is smallest
+ #
+ # | 2222222 |
+ # |----111111111--------------|
+ #
+ return (DOWNSTREAM if strand == '+' else UPSTREAM)
+ else:
+ # No overlap: region2 is downstream of region1
+ #
+ # | 2222222 |
+ # |-------------111111111-----|
+ #
+ return (UPSTREAM if strand == '+' else DOWNSTREAM)
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/distances.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/distances.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/output.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/output.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,589 @@
+#!/bin/env python
+#
+# output.py: functions for outputting analysis results
+# Copyright (C) University of Manchester 2015 Peter Briggs, Leo Zeef
+# & Ian Donaldson
+#
+"""
+output.py
+
+Functions for outputing analysis results
+
+"""
+import distances
+from Peaks import Peak
+import tempfile
+
+#######################################################################
+# Constants
+#######################################################################
+
+MULTI_LINE=0
+SINGLE_LINE=1
+FIELDS = {
+ 'chr': "chromosome",
+ 'start': "peak start position",
+ 'end': "peak end position",
+ 'id': "feature ID",
+ 'strand': "feature strand direction",
+ 'TSS': "feature TSS position",
+ 'TES': "feature TES position",
+ 'peak.chr': "chromosome of the peak",
+ 'peak.start': "peak start position",
+ 'peak.end': "peak end position",
+ 'feature.id': "feature ID",
+ 'feature.chr': "chromosome of the feature",
+ 'feature.start': "feature start position",
+ 'feature.end': "feature end position",
+ 'feature.TSS': "feature TSS position",
+ 'feature.TES': "feature TES position",
+ 'feature.strand': "feature strand direction",
+ 'dist_closest': "closest distance between peak and feature considering all edges (zero if there is overlap)",
+ 'dist_TSS': "distance between peak and feature TSS",
+ 'dist_TES': "distance between peak and feature TES",
+ 'overlap_feature': "1 if peak overlaps the feature, 0 if not",
+ 'overlap_promoter': "1 if peak overlaps the promoter region, 0 if not",
+ 'in_the_feature': "'YES' if peak overlaps the feature, 'NO' if not",
+ 'direction': "'U' if hit is upstream, 'D' if downstream, '.' if overlapped",
+ 'differentially_expressed': "1 if feature is differentially expressed, 0 if not",
+ 'order': "the 'order' of the feature/peak pair (e.g. '1 of 4')",
+ 'number_of_results': "number of hits being reported",
+}
+
+#######################################################################
+# Classes
+#######################################################################
+
+class AnalysisReporter:
+ """
+ Class to handle reporting of analysis results
+
+ Once initialised the reporter can be used to generate 'reports'
+ of each peak along with the nearest features (using the
+ 'report_nearest_features' method) or for each feature along
+ with the nearest peaks (using 'report_nearest_peaks').
+
+ Output can be in either 'multi-line' (one line per result pair),
+ or 'single-line' format (one line containing all results).
+
+ For each method a list of the fields to be reported can be
+ specified. Available fields are:
+
+ - (peak.)chr: chromosome for the peak
+ - (peak.)start: peak start position
+ - (peak.)end: peak end position
+ - (feature.)id: feature ID
+ - feature.chr: chromosome for the feature
+ - feature.start: feature start position
+ - feature.end: feature end position
+ - (feature.)TSS: feature TSS
+ - (feature.)TES: feature TES
+ - (feature.)strand: feature strand
+ - dist_closest: closest distance between peak and feature
+ - dist_TSS: distance between peak and feature TSS
+ - dist_TES: distance between peak and feature TES
+ - overlap_feature: 'YES' if peak overlaps the feature, 'NO' if not
+ - overlap_promoter: 1 if peak overlaps the promoter region, 0 if not
+ - in_the_feature: synonym for 'overlap_feature'
+ - 'differentially_expressed': flag value for feature
+
+ (In the field names above, the parts in (...) are optional e.g.
+ 'chr' == 'peak.chr' etc.)
+
+ For multi-line output these additional fields are available:
+
+ - order: the 'order' of the feature/peak pair (e.g. '1 of 4')
+
+ For single-line output these additional fields are available:
+
+ - number_of_results
+ - list(...): output all results (peaks or features, as
+ appropriate)
+
+ For the 'list' options, the paranthese should enclose a list
+ of fields to output for each peak or feature in the list e.g.
+ 'list(chr,start,dist_closest)' or 'list(feature.id)'.
+
+ The following fields have not been implemented:
+
+ - features_inbetween
+
+ """
+ def __init__(self,mode,fields,promoter_region=None,
+ max_hits=None,pad=False,
+ null_placeholder='.',
+ feature_type=None):
+ """
+ Create new AnalysisReporter instance
+
+ Arguments:
+ mode (int): either SINGLE_LINE or MULTI_LINE
+ fields (list): list of fields to output
+ promoter_region (tuple): promoter region extent (optional)
+ max_hits (int): optional maximum number of hits to
+ report for each set of results
+ null_placeholder (str): placeholder to use in output for
+ fields which evaluate to 'null'
+ pad (bool): add extra 'None' items to output hits to
+ pad out to max_closest results (n.b. padding is
+ always performed in SINGLE_LINE mode)
+ feature_type (str): if not 'None' then replace 'feature'
+ with 'feature_type' (e.g. 'gene', 'transcript' etc) in
+ the output
+
+ """
+ self._fields = fields
+ self._mode = mode
+ self._promoter_region = promoter_region
+ self._placeholder = null_placeholder
+ self._max_hits = max_hits
+ self._pad = pad
+ self._context_peak = None
+ self._context_feature = None
+ self._is_features = None
+ self._feature_type = feature_type
+ self._max_pairs = 0
+
+ def report_nearest(self,reference,results):
+ """
+ Return details of nearest objects to a reference
+
+ This is a generic reporting method which can handle
+ either nearest features to a reference peak (in which
+ case ``reference`` should be a Peak and ``results``
+ the corresponding FeatureSet), or nearest peaks to a
+ reference Feature (when ``reference`` is a Feature and
+ ``results`` is a PeakSet).
+
+ Arguments:
+ reference (Object): reference object (i.e.
+ Peak or Feature of interest)
+ results (Object): list of corresponding results
+ i.e. FeatureSet (for reference Peak) or
+ PeakSet (reference Feature)
+
+ Yields:
+ string: line(s) of text reporting the results
+
+ """
+ # Initialise and set the context
+ if isinstance(reference,Peak):
+ self._context_peak = reference
+ self._is_features = True
+ else:
+ self._context_feature = reference
+ self._is_features = False
+ is_features = self._is_features
+ # Store largest number of pairs reported
+ self._max_pairs = max(self._max_pairs,len(results))
+ # Reduce to maximum number of hits
+ if self._max_hits is not None:
+ results = results[:self._max_hits]
+ else:
+ results = results[:]
+ nresults = len(results)
+ # Pad with null results
+ if self._mode == SINGLE_LINE or self._pad:
+ while len(results) < self._max_hits:
+ if is_features:
+ results.addFeature(None)
+ else:
+ results.addPeak(None)
+ # Write the results
+ if self._mode == SINGLE_LINE:
+ # Report everything on a single line
+ line = []
+ for field in self._fields:
+ if field == 'number_of_results':
+ value = nresults
+ elif field.startswith('list('):
+ # Extract the subfields
+ subfields = field[:-1].split('(')[1].split(',')
+ # Report list of features
+ value = []
+ for result in results:
+ if is_features:
+ self._context_feature = result
+ else:
+ self._context_peak = result
+ for subfield in subfields:
+ value.append(self.value_for(subfield))
+ value = '\t'.join([str(x) for x in value])
+ else:
+ # All other fields
+ value = self.value_for(field)
+ line.append(str(value))
+ # Return (yield) the line
+ yield '\t'.join(line)
+ elif self._mode == MULTI_LINE:
+ # Report each result pair on a new line
+ i = 0
+ for result in results:
+ if is_features:
+ self._context_feature = result
+ else:
+ self._context_peak = result
+ i += 1
+ line = []
+ for field in self._fields:
+ if field == 'order' and result is not None:
+ value = '%d of %d' % (i,nresults)
+ else:
+ value = self.value_for(field)
+ line.append(str(value))
+ # Return (yield) the line
+ yield '\t'.join(line)
+ # Reset the context
+ self._context_peak = None
+ self._context_feature = None
+ self._is_features = None
+
+ def report_nearest_features(self,peak,features):
+ """
+ Return details of nearest features for a peak
+
+ This is a wrapper for ``report_nearest``.
+
+ Arguments:
+ peak (Peak): peak of interest
+ features (FeatureSet): list of nearest features
+
+ Yields:
+ string: line(s) of text reporting the results
+
+ """
+ for line in self.report_nearest(peak,features):
+ yield line
+
+ def report_nearest_peaks(self,feature,peaks):
+ """
+ Return details of nearest peaks for a feature
+
+ This is a wrapper for ``report_nearest``.
+
+ Arguments:
+ feature (Feature): feature of interest
+ peaks (PeakSet): list of nearest peaks
+
+ Returns:
+ string: block of text reporting the results
+
+ """
+ for line in self.report_nearest(feature,peaks):
+ yield line
+
+ def value_for(self,attr):
+ """
+ Return the value for the specified attribute
+
+ Wraps '_value_for' method, and returns the null
+ placeholder value in the event of an AttributeError
+ being raised.
+
+ Arguments:
+ attr (string): attribute name
+
+ Returns:
+ Value of the field for the current peak/feature
+ pair
+
+ """
+ try:
+ return self._value_for(attr)
+ except (AttributeError,KeyError):
+ return self._placeholder
+
+ def _value_for(self,attr):
+ """
+ Return the value for the specified attribute
+
+ Given the name of a field/attribute (see above for
+ a list and definition of each), return the value
+ for the current peak/feature pair (which should have
+ been set by the calling method in the '_context_peak'
+ and '_context_feature' properties).
+
+ Arguments:
+ attr (string): attribute name
+
+ Returns:
+ Value of the field for the current peak/feature
+ pair
+
+ Raises:
+ AttributeError: if valid ``attr`` cannot be derived
+ KeyError: if ``attr`` is not a recognised attribute
+ name
+
+ """
+ peak = self._context_peak
+ feature = self._context_feature
+ is_features = self._is_features
+ if attr == 'chr' or attr == 'peak.chr':
+ return peak.chrom
+ elif attr == 'peak.start' or attr == 'start':
+ return peak.start
+ elif attr == 'peak.end' or attr == 'end':
+ return peak.end
+ elif attr == 'id' or attr == 'feature.id':
+ return feature.id
+ elif attr == 'feature.chr':
+ return feature.chrom
+ elif attr == 'feature.start':
+ return feature.start
+ elif attr == 'feature.end':
+ return feature.end
+ elif attr == 'TSS':
+ return feature.tss
+ elif attr == 'TES':
+ return feature.tes
+ elif attr == 'strand' or attr == 'feature.strand':
+ return feature.strand
+ elif attr == 'differentially_expressed':
+ return feature.flag
+ elif attr == 'dist_closest':
+ return distances.distance_closest_edge(peak,feature)
+ elif attr == 'dist_TSS':
+ return distances.distance_tss(peak,feature)
+ elif attr == 'dist_TES':
+ return distances.distance_tes(peak,feature)
+ elif attr == 'overlap_feature' or attr == 'in_the_feature':
+ if distances.regions_overlap((peak.start,peak.end),
+ (feature.tss,feature.tes)):
+ overlap_feature = 1
+ else:
+ overlap_feature = 0
+ if attr == 'in_the_feature':
+ overlap_feature = ('YES' if overlap_feature == 1 else 'NO')
+ return overlap_feature
+ elif attr == 'overlap_promoter':
+ if self._promoter_region is not None:
+ promoter = feature.getPromoterRegion(*self._promoter_region)
+ if distances.regions_overlap((peak.start,peak.end),
+ promoter):
+ overlap_promoter = 1
+ else:
+ overlap_promoter = 0
+ else:
+ raise Exception("'overlap_promoter' requested but no "
+ "promoter region has been defined")
+ return overlap_promoter
+ elif attr == 'direction':
+ if self._is_features:
+ direction = distances.direction(feature,peak)
+ else:
+ direction = distances.direction(peak,feature)
+ if direction == distances.UPSTREAM:
+ return 'U'
+ elif direction == distances.DOWNSTREAM:
+ return 'D'
+ else:
+ return '.'
+ elif attr == 'features_inbetween':
+ raise NotImplementedError("'features_inbetween' not implemented")
+ else:
+ raise KeyError("Unrecognised report field: '%s'" % attr)
+
+ def make_header(self):
+ """
+ Create a 'header' line for output
+
+ Builds a header line which can be incorporated into
+ an output file, based on the fields that are being
+ reported.
+
+ Returns:
+ str: tab-delimited header line
+
+ """
+ if self._mode == MULTI_LINE:
+ if self._feature_type is None:
+ return '\t'.join(self._fields)
+ else:
+ return '\t'.join([x.replace('feature',self._feature_type)
+ for x in self._fields])
+ elif self._mode == SINGLE_LINE:
+ header_fields = []
+ if self._max_hits is not None:
+ max_pairs = self._max_hits
+ else:
+ max_pairs = self._max_pairs
+ for f in self._fields:
+ try:
+ # Handle fields in a list(...)
+ subfields = f[:-1].split('(')[1].split(',')
+ for i in range(1,max_pairs+1):
+ for s in subfields:
+ header_fields.append("%s_%d" % (s,i))
+ except IndexError:
+ # Not a list
+ header_fields.append(f)
+ if self._feature_type is not None:
+ header_fields = [x.replace('feature',self._feature_type)
+ for x in header_fields]
+ return '\t'.join(header_fields)
+
+class AnalysisReportWriter(AnalysisReporter):
+ """
+ Write analysis results to file
+
+ Wrapper for AnalysisReporter that writes the results to
+ a file; optionally it can also write 'summary' files
+ (only top result is reported).
+
+ """
+ def __init__(self,mode,fields,promoter_region=None,
+ null_placeholder='.',feature_type=None,
+ max_hits=None,pad=None,
+ outfile=None,summary=None):
+ """
+ Create new AnalysisReportWriter instance
+
+ Arguments:
+ mode (int): either SINGLE_LINE or MULTI_LINE
+ fields (list): list of fields to output
+ promoter_region (tuple): promoter region extent (optional)
+ null_placeholder (str): placeholder to use in output for
+ fields which evaluate to 'null'
+ feature_type (str): if not 'None' then replace 'feature'
+ with 'feature_type' (e.g. 'gene', 'transcript' etc) in
+ the output
+ max_hits (int): optional maximum number of hits to
+ report for each set of results
+ pad (bool): add extra 'None' items to output hits to
+ pad out to max_closest results
+ outfile (str): name of output file to write results to
+ summary (str): optional, name of file to write summary
+ results to
+
+ """
+ AnalysisReporter.__init__(self,mode,fields,
+ promoter_region=promoter_region,
+ null_placeholder=null_placeholder,
+ pad=pad,max_hits=max_hits,
+ feature_type=feature_type)
+ self.outfile = outfile
+ if self.outfile is not None:
+ # Open temporary file to handle output
+ self._fp = tempfile.TemporaryFile()
+ else:
+ self._fp = None
+ self.summary = summary
+ if self.summary is not None:
+ # Open temporary file to handle summary
+ self._summary = tempfile.TemporaryFile()
+ else:
+ self._summary = None
+
+ def write_nearest_features(self,peak,features):
+ """
+ Write a set of features to the output file(s)
+
+ Arguments:
+ peak (Peak): peak of interest
+ features (FeatureSet): list of nearest features
+
+ """
+ lines = list(self.report_nearest_features(peak,features))
+ if self._fp is not None:
+ self._fp.write("%s\n" % '\n'.join(lines))
+ if self._summary is not None:
+ self._summary.write("%s\n" % lines[0])
+
+ def write_nearest_peaks(self,feature,peaks):
+ """
+ Write a set of peaks to the output file(s)
+
+ Arguments:
+ feature (Feature): feature of interest
+ peaks (PeakSet): list of nearest peaks
+
+ """
+ lines = list(self.report_nearest_peaks(feature,peaks))
+ if self._fp is not None:
+ self._fp.write("%s\n" % '\n'.join(lines))
+ if self._summary is not None:
+ self._summary.write("%s\n" % lines[0])
+
+ def close(self):
+ """
+ Close the files associated with the writer
+
+ In reality the data has been written to temporary
+ files; the purpose of this method is to open,
+ write and close the final 'visible' output files.
+
+ """
+ # Full output file
+ if self.outfile:
+ # Rewind to the start of the temp file
+ self._fp.seek(0)
+ # Write the final output file
+ with open(self.outfile,'w') as fp:
+ # Write the header
+ fp.write("#%s\n" % self.make_header())
+ # Write the content
+ nitems = len(self.make_header().split('\t'))
+ for line in self._fp:
+ if self._mode == SINGLE_LINE:
+ # Handle padding trailing empty fields
+ fields = line.rstrip().split('\t')
+ while len(fields) < nitems:
+ fields.append(self._placeholder)
+ line = '\t'.join(fields) + '\n'
+ fp.write(line)
+ # Dispose of the temp file
+ self._fp.close()
+ # Summary output file
+ if self.summary:
+ # Rewind to the start of the temp file
+ self._summary.seek(0)
+ # Write the final summary file
+ with open(self.summary,'w') as fp:
+ # Write the header
+ fp.write("#%s\n" % self.make_header())
+ # Write the content
+ for line in self._summary:
+ fp.write(line)
+ # Dispose of the temp file
+ self._summary.close()
+
+def describe_fields(fields):
+ """
+ Return list of field descriptions
+
+ Creates a list consisting of (FIELD,DESC) tuples
+ where FIELD is the name of the field and DESC is
+ its corresponding description text.
+
+ For example if the supplied fields were:
+
+ "chr,start,id,dist_closest"
+
+ then the resulting desciption list would look like:
+
+ [('chr','Chromosome'),
+ ('start','Peak start position'),
+ ('id','Feature ID'),
+ ('dist_closest','Closest distance between peak and feature')]
+
+ Arguments:
+ fields (list): list of fields
+
+ Returns:
+ list: list of (field,description) tuples.
+
+ """
+ descriptions = []
+ for attr in fields:
+ try:
+ descriptions.append(("%s" % attr,
+ "%s" % FIELDS[attr]))
+ except KeyError:
+ if attr.startswith('list('):
+ descriptions.append(('For each hit:',))
+ sub_attrs = attr[:-1].split('(')[1].split(',')
+ for sub_attr in sub_attrs:
+ descriptions.append(("%s_#" % sub_attr,
+ "%s" % FIELDS[sub_attr]))
+ return descriptions
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/output.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/output.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/utils.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/utils.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,62 @@
+#!/bin/env python
+#
+# utils.py: utility functions for RnaChipIntegrator
+# Copyright (C) University of Manchester 2011-15 Peter Briggs, Leo Zeef
+# & Ian Donaldson
+#
+"""
+utils.py
+
+Utility functions for RnaChipIntegrator:
+
+- make_errline: highlight problem fields in a string
+- truncate_text: truncate a text string to a specified length
+
+"""
+
+def make_errline(line,bad_fields=[]):
+ """Return an 'error line' indicating problem fields in a string
+
+ Given a tab-delimited line and a list of integer indices
+ indicating which fields in the line have problems, this function
+ returns a tab-delimited string where the original fields are
+ replaced by either spaces or '^' characters.
+
+ When printed beneath the original line, the '^'s indicate which
+ fields are 'bad' according to the supplied indices, e.g.
+
+ Input line: 'good good bad bad good'
+ Error line: ' ^^^ ^^^ '
+
+ Arguments:
+ line: string where tabs delimit fields
+ bad_fields: list of integer indices corresponding to 'bad'
+ values in 'line'
+
+ Returns:
+ Tab-delimited 'error line' to be printed beneath the original
+ line, to indicate which fields are 'bad'.
+ """
+ # Indicate problem field(s)
+ errline = []
+ items = line.rstrip().split('\t')
+ for i in range(len(items)):
+ if i in bad_fields:
+ errline.append("^"*len(items[i]))
+ else:
+ errline.append(" "*len(items[i]))
+ return '\t'.join(errline)
+
+def truncate_text(text,max_len):
+ """Truncate a text string
+
+ Given a title and an optional extension, remove characters
+ and replace with ellipsis (i.e. ...) so that it fit into
+ the maxium number of characters (max_len).
+
+ """
+ len_text = len(text)
+ if len_text <= max_len:
+ return text
+ text = text[len_text-max_len:]
+ return '...' + text[3:]
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/utils.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/utils.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/xls_output.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/xls_output.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,270 @@
+#!/bin/env python
+#
+# xls_output.py: functions for writing analysis results to Excel files
+# Copyright (C) University of Manchester 2015-16 Peter Briggs, Leo Zeef
+# & Ian Donaldson
+#
+"""
+xls_output.py
+
+Functions for outputting analysis results to XLSX spreadsheet
+
+"""
+import datetime
+import xlsxwriter
+import re
+import output
+import utils
+
+# Regular expressions for styling tags
+RE_STYLE = re.compile(r"^$")
+
+# Notes text
+NOTES = dict()
+NOTES['preamble'] = """
+
+Find nearest peaks to %ss (and vice versa)
+
+Bioinformatics Core Facility, Faculty of Life Sciences, University of Manchester
+http://fls-bioinformatics-core.github.com/RnaChipIntegrator/
+Run on %s
+
+"""
+NOTES['peak_centric'] = """
+
+Column\tDescription"""
+NOTES['feature_centric'] = """
+
+Column\tDescription"""
+
+class XLSX:
+ """
+ Class to assemble XLSX output file
+
+ Utility class to help build an XLSX file from existing
+ output TSV files.
+
+ Example usage:
+
+ >>> xlsx = XLS('results.xlsx')
+ >>> xlsx.add_result_sheet('results','results.tsv')
+ >>> xlsx.write()
+
+ """
+ def __init__(self,xlsx_file,program_version,feature_type=None):
+ """
+ Create a new XLSX instance
+
+ Arguments:
+ xlsx_file (str): name or path of output file
+ program_version (str): name and version of the program
+ that is writing the spreadsheet
+ feature_type (str): if not None then replace 'feature'
+ with 'feature_type' (e.g. 'gene', 'transcript' etc) in
+ the output
+
+ """
+ self._xlsx = xlsxwriter.Workbook(xlsx_file)
+ self._sheets = {}
+ self._rows = {}
+ self._widths = {}
+ self._styles = {}
+ self._feature_type = ('gene' if feature_type is None
+ else feature_type)
+ self.add_sheet("Notes")
+ self.append_to_notes(NOTES['preamble'] % (program_version,
+ self._feature_type,
+ datetime.date.today()))
+
+ def add_sheet(self,name):
+ """
+ Create a new worksheet in the XLSX file
+
+ Arguments:
+ name (str): title for the new sheet (must be
+ unique across the XLSX file)
+
+ Returns:
+ WorkSheet: new worksheet.
+
+ """
+ if name in self._sheets:
+ raise KeyError("'%s': worksheet already exists")
+ ws = self._xlsx.add_worksheet(name)
+ self._sheets[name] = ws
+ self._rows[name] = 0
+ self._widths[name] = []
+ return ws
+
+ def get_format(self,*args):
+ """
+ Return a cell format object matching arguments
+
+ Returns a Format object matching the supplied
+ arguments, which should be strings of the form
+
+ 'KEY=VALUE'
+
+ Formats are cached so there will be one Format
+ per unique set of key/value pairs.
+
+ """
+ # Create a name for this style
+ name = list(args)[:]
+ name.sort()
+ name = "_".join(name)
+ # See if it's already defined
+ if name not in self._styles:
+ # Create a new style (cell_format)
+ fmt = self._xlsx.add_format()
+ for style in args:
+ if style == "font=bold":
+ fmt.set_bold(True)
+ elif style.startswith("bgcolor="):
+ color = style.split('=')[1]
+ fmt.set_bg_color(color)
+ else:
+ raise NotImplementedError("%s: not implemented" %
+ style)
+ self._styles[name] = fmt
+ # Return the cell format for this style
+ return self._styles[name]
+
+ def add_text(self,name,text):
+ """
+ Add (append) arbitrary text to a worksheet
+
+ Arguments:
+ name (str): name of the worksheet
+ text (str): text that will be added to the
+ end of the worksheet
+
+ """
+ ws = self._sheets[name]
+ i = self._rows[name]
+ for line in text.split('\n'):
+ j = 0
+ for item in line.split('\t'):
+ # Check for styles
+ style_match = RE_STYLE.match(item)
+ if style_match:
+ item = style_match.group(2)
+ style = style_match.group(1).split()
+ fmt = self.get_format(*style)
+ else:
+ fmt = None
+ # Write the item
+ ws.write(i,j,item,fmt)
+ # Update the widths
+ try:
+ self._widths[name][j] = max(self._widths[name][j],
+ len(item))
+ except IndexError:
+ self._widths[name].append(len(item))
+ # Increment column counter
+ j += 1
+ # Increment row counter
+ i += 1
+ self._rows[name] = i
+
+ def append_to_notes(self,text):
+ """
+ Append arbitrary text to the 'notes' page
+
+ Arguments:
+ text (str): text that will be added to the
+ end of the notes.
+
+ """
+ self.add_text("Notes",text)
+
+ def write_peak_centric(self,fields):
+ """
+ Write details of the 'peak-centric' results to XLSX notes
+
+ Arguments:
+ fields (list): list of fields in the output
+
+ """
+ self.append_to_notes(NOTES['peak_centric'] %
+ self._feature_type)
+ self.append_to_notes(self._field_descriptions(fields))
+
+ def write_feature_centric(self,fields):
+ """
+ Write details of the 'feature-centric' results to XLSX notes
+
+ Arguments:
+ fields (list): list of fields in the output
+
+ """
+ self.append_to_notes(NOTES['feature_centric'] %
+ (self._feature_type.title(),
+ self._feature_type))
+ self.append_to_notes(self._field_descriptions(fields))
+
+ def _field_descriptions(self,fields):
+ """
+ Generate field (column) descriptions for XLSX notes
+
+ Arguments:
+ fields (list): list of fields to describe
+
+ Returns:
+ string: text with one field name/description pair
+ (separated by a tab) per line
+
+ """
+ return '\n'.join(['\t'.join(x) for x in
+ output.describe_fields(fields)]).\
+ replace('feature',self._feature_type).\
+ replace('Feature',self._feature_type.title())
+
+ def add_result_sheet(self,title,tsv_file):
+ """
+ Add a sheet populated from a file
+
+ Creates a new sheet in the spreadsheet with the
+ supplied title and populates using the contents
+ of a tab-delimited file.
+
+ If there are more lines than can be written to a
+ single worksheet then creates additional sheets
+ as required.
+
+ Arguments:
+ title (str): a title for the sheet
+ tsv_file (str): path to a tab-delimited file
+
+ """
+ ws = self.add_sheet(title)
+ # Get header line
+ with open(tsv_file,'r') as fp:
+ i = self._rows[title]
+ for line in fp:
+ j = 0
+ for value in line.rstrip('\n').split('\t'):
+ ws.write(i,j,value)
+ try:
+ self._widths[title][j] = max(self._widths[title][j],
+ len(value))
+ except IndexError:
+ self._widths[title].append(len(value))
+ j += 1
+ i += 1
+ self._rows[title] = i
+ # Freeze the header
+ ws.freeze_panes(1,0)
+
+ def write(self):
+ """
+ Write XLSX to file
+
+ """
+ # Set the column widths
+ for name in self._sheets:
+ ws = self._sheets[name]
+ for j,w in enumerate(self._widths[name]):
+ ws.set_column(j,j,w*1.2)
+ # Close to write to file
+ self._xlsx.close()
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/xls_output.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/rnachipintegrator/xls_output.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/__init__.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/__init__.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,3 @@
+__version__ = '0.8.4'
+__VERSION__ = __version__
+from .workbook import Workbook
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/__init__.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/__init__.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/app.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/app.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,196 @@
+###############################################################################
+#
+# App - A class for writing the Excel XLSX App file.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+# Package imports.
+from . import xmlwriter
+
+
+class App(xmlwriter.XMLwriter):
+ """
+ A class for writing the Excel XLSX App file.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self):
+ """
+ Constructor.
+
+ """
+
+ super(App, self).__init__()
+
+ self.part_names = []
+ self.heading_pairs = []
+ self.properties = {}
+
+ def _add_part_name(self, part_name):
+ # Add the name of a workbook Part such as 'Sheet1' or 'Print_Titles'.
+ self.part_names.append(part_name)
+
+ def _add_heading_pair(self, heading_pair):
+ # Add the name of a workbook Heading Pair such as 'Worksheets',
+ # 'Charts' or 'Named Ranges'.
+
+ # Ignore empty pairs such as chartsheets.
+ if not heading_pair[1]:
+ return
+
+ self.heading_pairs.append(('lpstr', heading_pair[0]))
+ self.heading_pairs.append(('i4', heading_pair[1]))
+
+ def _set_properties(self, properties):
+ # Set the document properties.
+ self.properties = properties
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _assemble_xml_file(self):
+ # Assemble and write the XML file.
+
+ # Write the XML declaration.
+ self._xml_declaration()
+
+ self._write_properties()
+ self._write_application()
+ self._write_doc_security()
+ self._write_scale_crop()
+ self._write_heading_pairs()
+ self._write_titles_of_parts()
+ self._write_manager()
+ self._write_company()
+ self._write_links_up_to_date()
+ self._write_shared_doc()
+ self._write_hyperlink_base()
+ self._write_hyperlinks_changed()
+ self._write_app_version()
+
+ self._xml_end_tag('Properties')
+
+ # Close the file.
+ self._xml_close()
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_properties(self):
+ # Write the element.
+ schema = 'http://schemas.openxmlformats.org/officeDocument/2006/'
+ xmlns = schema + 'extended-properties'
+ xmlns_vt = schema + 'docPropsVTypes'
+
+ attributes = [
+ ('xmlns', xmlns),
+ ('xmlns:vt', xmlns_vt),
+ ]
+
+ self._xml_start_tag('Properties', attributes)
+
+ def _write_application(self):
+ # Write the element.
+ self._xml_data_element('Application', 'Microsoft Excel')
+
+ def _write_doc_security(self):
+ # Write the element.
+ self._xml_data_element('DocSecurity', '0')
+
+ def _write_scale_crop(self):
+ # Write the element.
+ self._xml_data_element('ScaleCrop', 'false')
+
+ def _write_heading_pairs(self):
+ # Write the element.
+ self._xml_start_tag('HeadingPairs')
+ self._write_vt_vector('variant', self.heading_pairs)
+ self._xml_end_tag('HeadingPairs')
+
+ def _write_titles_of_parts(self):
+ # Write the element.
+ parts_data = []
+
+ self._xml_start_tag('TitlesOfParts')
+
+ for part_name in self.part_names:
+ parts_data.append(('lpstr', part_name))
+
+ self._write_vt_vector('lpstr', parts_data)
+
+ self._xml_end_tag('TitlesOfParts')
+
+ def _write_vt_vector(self, base_type, vector_data):
+ # Write the element.
+ attributes = [
+ ('size', len(vector_data)),
+ ('baseType', base_type),
+ ]
+
+ self._xml_start_tag('vt:vector', attributes)
+
+ for vt_data in vector_data:
+ if base_type == 'variant':
+ self._xml_start_tag('vt:variant')
+
+ self._write_vt_data(vt_data)
+
+ if base_type == 'variant':
+ self._xml_end_tag('vt:variant')
+
+ self._xml_end_tag('vt:vector')
+
+ def _write_vt_data(self, vt_data):
+ # Write the elements such as and .
+ self._xml_data_element("vt:%s" % vt_data[0], vt_data[1])
+
+ def _write_company(self):
+ company = self.properties.get('company', '')
+
+ self._xml_data_element('Company', company)
+
+ def _write_manager(self):
+ # Write the element.
+ if 'manager' not in self.properties:
+ return
+
+ self._xml_data_element('Manager', self.properties['manager'])
+
+ def _write_links_up_to_date(self):
+ # Write the element.
+ self._xml_data_element('LinksUpToDate', 'false')
+
+ def _write_shared_doc(self):
+ # Write the element.
+ self._xml_data_element('SharedDoc', 'false')
+
+ def _write_hyperlink_base(self):
+ # Write the element.
+ hyperlink_base = self.properties.get('hyperlink_base')
+
+ if hyperlink_base is None:
+ return
+
+ self._xml_data_element('HyperlinkBase', hyperlink_base)
+
+ def _write_hyperlinks_changed(self):
+ # Write the element.
+ self._xml_data_element('HyperlinksChanged', 'false')
+
+ def _write_app_version(self):
+ # Write the element.
+ self._xml_data_element('AppVersion', '12.0000')
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/app.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/app.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,3906 @@
+###############################################################################
+#
+# Chart - A class for writing the Excel XLSX Worksheet file.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+import re
+import copy
+from warnings import warn
+
+from .shape import Shape
+from . import xmlwriter
+from .utility import get_rgb_color
+from .utility import xl_rowcol_to_cell
+from .utility import xl_range_formula
+from .utility import supported_datetime
+from .utility import datetime_to_excel_datetime
+from .utility import quote_sheetname
+
+
+class Chart(xmlwriter.XMLwriter):
+ """
+ A class for writing the Excel XLSX Chart file.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self, options=None):
+ """
+ Constructor.
+
+ """
+
+ super(Chart, self).__init__()
+
+ self.subtype = None
+ self.sheet_type = 0x0200
+ self.orientation = 0x0
+ self.series = []
+ self.embedded = 0
+ self.id = -1
+ self.series_index = 0
+ self.style_id = 2
+ self.axis_ids = []
+ self.axis2_ids = []
+ self.cat_has_num_fmt = 0
+ self.requires_category = False
+ self.legend_position = 'right'
+ self.legend_delete_series = None
+ self.legend_font = None
+ self.legend_layout = None
+ self.cat_axis_position = 'b'
+ self.val_axis_position = 'l'
+ self.formula_ids = {}
+ self.formula_data = []
+ self.horiz_cat_axis = 0
+ self.horiz_val_axis = 1
+ self.protection = 0
+ self.chartarea = {}
+ self.plotarea = {}
+ self.x_axis = {}
+ self.y_axis = {}
+ self.y2_axis = {}
+ self.x2_axis = {}
+ self.chart_name = ''
+ self.show_blanks = 'gap'
+ self.show_hidden = 0
+ self.show_crosses = 1
+ self.width = 480
+ self.height = 288
+ self.x_scale = 1
+ self.y_scale = 1
+ self.x_offset = 0
+ self.y_offset = 0
+ self.table = None
+ self.cross_between = 'between'
+ self.default_marker = None
+ self.series_gap_1 = None
+ self.series_gap_2 = None
+ self.series_overlap_1 = None
+ self.series_overlap_2 = None
+ self.drop_lines = None
+ self.hi_low_lines = None
+ self.up_down_bars = None
+ self.smooth_allowed = False
+ self.title_font = None
+ self.title_name = None
+ self.title_formula = None
+ self.title_data_id = None
+ self.title_layout = None
+ self.title_overlay = None
+ self.title_none = False
+ self.date_category = False
+ self.date_1904 = False
+ self.label_positions = {}
+ self.label_position_default = ''
+ self.already_inserted = False
+ self.combined = None
+ self.is_secondary = False
+ self._set_default_properties()
+
+ def add_series(self, options):
+ """
+ Add a data series to a chart.
+
+ Args:
+ options: A dictionary of chart series options.
+
+ Returns:
+ Nothing.
+
+ """
+ # Add a series and it's properties to a chart.
+
+ # Check that the required input has been specified.
+ if 'values' not in options:
+ warn("Must specify 'values' in add_series()")
+ return
+
+ if self.requires_category and 'categories' not in options:
+ warn("Must specify 'categories' in add_series() "
+ "for this chart type")
+
+ # Convert list into a formula string.
+ values = self._list_to_formula(options.get('values'))
+ categories = self._list_to_formula(options.get('categories'))
+
+ # Switch name and name_formula parameters if required.
+ name, name_formula = self._process_names(options.get('name'),
+ options.get('name_formula'))
+
+ # Get an id for the data equivalent to the range formula.
+ cat_id = self._get_data_id(categories, options.get('categories_data'))
+ val_id = self._get_data_id(values, options.get('values_data'))
+ name_id = self._get_data_id(name_formula, options.get('name_data'))
+
+ # Set the line properties for the series.
+ line = Shape._get_line_properties(options.get('line'))
+
+ # Allow 'border' as a synonym for 'line' in bar/column style charts.
+ if options.get('border'):
+ line = Shape._get_line_properties(options['border'])
+
+ # Set the fill properties for the series.
+ fill = Shape._get_fill_properties(options.get('fill'))
+
+ # Set the pattern fill properties for the series.
+ pattern = Shape._get_pattern_properties(options.get('pattern'))
+
+ # Set the gradient fill properties for the series.
+ gradient = Shape._get_gradient_properties(options.get('gradient'))
+
+ # Pattern fill overrides solid fill.
+ if pattern:
+ self.fill = None
+
+ # Gradient fill overrides the solid and pattern fill.
+ if gradient:
+ pattern = None
+ fill = None
+
+ # Set the marker properties for the series.
+ marker = self._get_marker_properties(options.get('marker'))
+
+ # Set the trendline properties for the series.
+ trendline = self._get_trendline_properties(options.get('trendline'))
+
+ # Set the line smooth property for the series.
+ smooth = options.get('smooth')
+
+ # Set the error bars properties for the series.
+ y_error_bars = self._get_error_bars_props(options.get('y_error_bars'))
+ x_error_bars = self._get_error_bars_props(options.get('x_error_bars'))
+
+ error_bars = {'x_error_bars': x_error_bars,
+ 'y_error_bars': y_error_bars}
+
+ # Set the point properties for the series.
+ points = self._get_points_properties(options.get('points'))
+
+ # Set the labels properties for the series.
+ labels = self._get_labels_properties(options.get('data_labels'))
+
+ # Set the "invert if negative" fill property.
+ invert_if_neg = options.get('invert_if_negative', False)
+
+ # Set the secondary axis properties.
+ x2_axis = options.get('x2_axis')
+ y2_axis = options.get('y2_axis')
+
+ # Store secondary status for combined charts.
+ if x2_axis or y2_axis:
+ self.is_secondary = True
+
+ # Set the gap for Bar/Column charts.
+ if options.get('gap') is not None:
+ if y2_axis:
+ self.series_gap_2 = options['gap']
+ else:
+ self.series_gap_1 = options['gap']
+
+ # Set the overlap for Bar/Column charts.
+ if options.get('overlap'):
+ if y2_axis:
+ self.series_overlap_2 = options['overlap']
+ else:
+ self.series_overlap_1 = options['overlap']
+
+ # Add the user supplied data to the internal structures.
+ series = {
+ 'values': values,
+ 'categories': categories,
+ 'name': name,
+ 'name_formula': name_formula,
+ 'name_id': name_id,
+ 'val_data_id': val_id,
+ 'cat_data_id': cat_id,
+ 'line': line,
+ 'fill': fill,
+ 'pattern': pattern,
+ 'gradient': gradient,
+ 'marker': marker,
+ 'trendline': trendline,
+ 'labels': labels,
+ 'invert_if_neg': invert_if_neg,
+ 'x2_axis': x2_axis,
+ 'y2_axis': y2_axis,
+ 'points': points,
+ 'error_bars': error_bars,
+ 'smooth': smooth
+ }
+
+ self.series.append(series)
+
+ def set_x_axis(self, options):
+ """
+ Set the chart X axis options.
+
+ Args:
+ options: A dictionary of axis options.
+
+ Returns:
+ Nothing.
+
+ """
+ axis = self._convert_axis_args(self.x_axis, options)
+
+ self.x_axis = axis
+
+ def set_y_axis(self, options):
+ """
+ Set the chart Y axis options.
+
+ Args:
+ options: A dictionary of axis options.
+
+ Returns:
+ Nothing.
+
+ """
+ axis = self._convert_axis_args(self.y_axis, options)
+
+ self.y_axis = axis
+
+ def set_x2_axis(self, options):
+ """
+ Set the chart secondary X axis options.
+
+ Args:
+ options: A dictionary of axis options.
+
+ Returns:
+ Nothing.
+
+ """
+ axis = self._convert_axis_args(self.x2_axis, options)
+
+ self.x2_axis = axis
+
+ def set_y2_axis(self, options):
+ """
+ Set the chart secondary Y axis options.
+
+ Args:
+ options: A dictionary of axis options.
+
+ Returns:
+ Nothing.
+
+ """
+ axis = self._convert_axis_args(self.y2_axis, options)
+
+ self.y2_axis = axis
+
+ def set_title(self, options):
+ """
+ Set the chart title options.
+
+ Args:
+ options: A dictionary of chart title options.
+
+ Returns:
+ Nothing.
+
+ """
+ name, name_formula = self._process_names(options.get('name'),
+ options.get('name_formula'))
+
+ data_id = self._get_data_id(name_formula, options.get('data'))
+
+ self.title_name = name
+ self.title_formula = name_formula
+ self.title_data_id = data_id
+
+ # Set the font properties if present.
+ self.title_font = self._convert_font_args(options.get('name_font'))
+
+ # Set the axis name layout.
+ self.title_layout = self._get_layout_properties(options.get('layout'),
+ True)
+ # Set the title overlay option.
+ self.title_overlay = options.get('overlay')
+
+ # Set the automatic title option.
+ self.title_none = options.get('none')
+
+ def set_legend(self, options):
+ """
+ Set the chart legend options.
+
+ Args:
+ options: A dictionary of chart legend options.
+
+ Returns:
+ Nothing.
+ """
+ self.legend_position = options.get('position', 'right')
+ self.legend_delete_series = options.get('delete_series')
+ self.legend_font = self._convert_font_args(options.get('font'))
+ self.legend_layout = self._get_layout_properties(options.get('layout'),
+ False)
+ # Turn off the legend.
+ if options.get('none'):
+ self.legend_position = 'none'
+
+ def set_plotarea(self, options):
+ """
+ Set the chart plot area options.
+
+ Args:
+ options: A dictionary of chart plot area options.
+
+ Returns:
+ Nothing.
+ """
+ # Convert the user defined properties to internal properties.
+ self.plotarea = self._get_area_properties(options)
+
+ def set_chartarea(self, options):
+ """
+ Set the chart area options.
+
+ Args:
+ options: A dictionary of chart area options.
+
+ Returns:
+ Nothing.
+ """
+ # Convert the user defined properties to internal properties.
+ self.chartarea = self._get_area_properties(options)
+
+ def set_style(self, style_id):
+ """
+ Set the chart style type.
+
+ Args:
+ style_id: An int representing the chart style.
+
+ Returns:
+ Nothing.
+ """
+ # Set one of the 48 built-in Excel chart styles. The default is 2.
+ if style_id is None:
+ style_id = 2
+
+ if style_id < 0 or style_id > 48:
+ style_id = 2
+
+ self.style_id = style_id
+
+ def show_blanks_as(self, option):
+ """
+ Set the option for displaying blank data in a chart.
+
+ Args:
+ option: A string representing the display option.
+
+ Returns:
+ Nothing.
+ """
+ if not option:
+ return
+
+ valid_options = {
+ 'gap': 1,
+ 'zero': 1,
+ 'span': 1,
+ }
+
+ if option not in valid_options:
+ warn("Unknown show_blanks_as() option '%s'" % option)
+ return
+
+ self.show_blanks = option
+
+ def show_hidden_data(self):
+ """
+ Display data on charts from hidden rows or columns.
+
+ Args:
+ option: A string representing the display option.
+
+ Returns:
+ Nothing.
+ """
+ self.show_hidden = 1
+
+ def set_size(self, options):
+ """
+ Set size or scale of the chart.
+
+ Args:
+ options: A dictionary of chart size options.
+
+ Returns:
+ Nothing.
+ """
+
+ # Set dimensions or scale for the chart.
+ self.width = options.get('width', self.width)
+ self.height = options.get('height', self.height)
+ self.x_scale = options.get('x_scale', 1)
+ self.y_scale = options.get('y_scale', 1)
+ self.x_offset = options.get('x_offset', 0)
+ self.y_offset = options.get('y_offset', 0)
+
+ def set_table(self, options=None):
+ """
+ Set properties for an axis data table.
+
+ Args:
+ options: A dictionary of axis table options.
+
+ Returns:
+ Nothing.
+
+ """
+ if options is None:
+ options = {}
+
+ table = {}
+
+ table['horizontal'] = options.get('horizontal', 1)
+ table['vertical'] = options.get('vertical', 1)
+ table['outline'] = options.get('outline', 1)
+ table['show_keys'] = options.get('show_keys', 0)
+
+ self.table = table
+
+ def set_up_down_bars(self, options=None):
+ """
+ Set properties for the chart up-down bars.
+
+ Args:
+ options: A dictionary of options.
+
+ Returns:
+ Nothing.
+
+ """
+ if options is None:
+ options = {}
+
+ # Defaults.
+ up_line = None
+ up_fill = None
+ down_line = None
+ down_fill = None
+
+ # Set properties for 'up' bar.
+ if options.get('up'):
+ if 'border' in options['up']:
+ # Map border to line.
+ up_line = Shape._get_line_properties(options['up']['border'])
+
+ if 'line' in options['up']:
+ up_line = Shape._get_line_properties(options['up']['line'])
+
+ if 'fill' in options['up']:
+ up_fill = Shape._get_line_properties(options['up']['fill'])
+
+ # Set properties for 'down' bar.
+ if options.get('down'):
+ if 'border' in options['down']:
+ # Map border to line.
+ down_line = \
+ Shape._get_line_properties(options['down']['border'])
+
+ if 'line' in options['down']:
+ down_line = Shape._get_line_properties(options['down']['line'])
+
+ if 'fill' in options['down']:
+ down_fill = Shape._get_line_properties(options['down']['fill'])
+
+ self.up_down_bars = {'up': {'line': up_line,
+ 'fill': up_fill,
+ },
+ 'down': {'line': down_line,
+ 'fill': down_fill,
+ },
+ }
+
+ def set_drop_lines(self, options=None):
+ """
+ Set properties for the chart drop lines.
+
+ Args:
+ options: A dictionary of options.
+
+ Returns:
+ Nothing.
+
+ """
+ if options is None:
+ options = {}
+
+ line = Shape._get_line_properties(options.get('line'))
+ fill = Shape._get_fill_properties(options.get('fill'))
+
+ # Set the pattern fill properties for the series.
+ pattern = Shape._get_pattern_properties(options.get('pattern'))
+
+ # Set the gradient fill properties for the series.
+ gradient = Shape._get_gradient_properties(options.get('gradient'))
+
+ # Pattern fill overrides solid fill.
+ if pattern:
+ self.fill = None
+
+ # Gradient fill overrides the solid and pattern fill.
+ if gradient:
+ pattern = None
+ fill = None
+
+ self.drop_lines = {'line': line,
+ 'fill': fill,
+ 'pattern': pattern,
+ 'gradient': gradient}
+
+ def set_high_low_lines(self, options=None):
+ """
+ Set properties for the chart high-low lines.
+
+ Args:
+ options: A dictionary of options.
+
+ Returns:
+ Nothing.
+
+ """
+ if options is None:
+ options = {}
+
+ line = Shape._get_line_properties(options.get('line'))
+ fill = Shape._get_fill_properties(options.get('fill'))
+
+ # Set the pattern fill properties for the series.
+ pattern = Shape._get_pattern_properties(options.get('pattern'))
+
+ # Set the gradient fill properties for the series.
+ gradient = Shape._get_gradient_properties(options.get('gradient'))
+
+ # Pattern fill overrides solid fill.
+ if pattern:
+ self.fill = None
+
+ # Gradient fill overrides the solid and pattern fill.
+ if gradient:
+ pattern = None
+ fill = None
+
+ self.hi_low_lines = {'line': line,
+ 'fill': fill,
+ 'pattern': pattern,
+ 'gradient': gradient}
+
+ def combine(self, chart=None):
+ """
+ Create a combination chart with a secondary chart.
+
+ Args:
+ chart: The secondary chart to combine with the primary chart.
+
+ Returns:
+ Nothing.
+
+ """
+ if chart is None:
+ return
+
+ self.combined = chart
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _assemble_xml_file(self):
+ # Assemble and write the XML file.
+
+ # Write the XML declaration.
+ self._xml_declaration()
+
+ # Write the c:chartSpace element.
+ self._write_chart_space()
+
+ # Write the c:lang element.
+ self._write_lang()
+
+ # Write the c:style element.
+ self._write_style()
+
+ # Write the c:protection element.
+ self._write_protection()
+
+ # Write the c:chart element.
+ self._write_chart()
+
+ # Write the c:spPr element for the chartarea formatting.
+ self._write_sp_pr(self.chartarea)
+
+ # Write the c:printSettings element.
+ if self.embedded:
+ self._write_print_settings()
+
+ # Close the worksheet tag.
+ self._xml_end_tag('c:chartSpace')
+ # Close the file.
+ self._xml_close()
+
+ def _convert_axis_args(self, axis, user_options):
+ # Convert user defined axis values into private hash values.
+ options = axis['defaults'].copy()
+ options.update(user_options)
+
+ name, name_formula = self._process_names(options.get('name'),
+ options.get('name_formula'))
+
+ data_id = self._get_data_id(name_formula, options.get('data'))
+
+ axis = {
+ 'defaults': axis['defaults'],
+ 'name': name,
+ 'formula': name_formula,
+ 'data_id': data_id,
+ 'reverse': options.get('reverse'),
+ 'min': options.get('min'),
+ 'max': options.get('max'),
+ 'minor_unit': options.get('minor_unit'),
+ 'major_unit': options.get('major_unit'),
+ 'minor_unit_type': options.get('minor_unit_type'),
+ 'major_unit_type': options.get('major_unit_type'),
+ 'display_units': options.get('display_units'),
+ 'log_base': options.get('log_base'),
+ 'crossing': options.get('crossing'),
+ 'position_axis': options.get('position_axis'),
+ 'position': options.get('position'),
+ 'label_position': options.get('label_position'),
+ 'num_format': options.get('num_format'),
+ 'num_format_linked': options.get('num_format_linked'),
+ 'interval_unit': options.get('interval_unit'),
+ 'interval_tick': options.get('interval_tick'),
+ 'text_axis': False,
+ }
+
+ if 'visible' in options:
+ axis['visible'] = options.get('visible')
+ else:
+ axis['visible'] = 1
+
+ # Convert the display units.
+ axis['display_units'] = self._get_display_units(axis['display_units'])
+ axis['display_units_visible'] = \
+ options.get('display_units_visible', True)
+
+ # Map major_gridlines properties.
+ if (options.get('major_gridlines')
+ and options['major_gridlines']['visible']):
+ axis['major_gridlines'] = \
+ self._get_gridline_properties(options['major_gridlines'])
+
+ # Map minor_gridlines properties.
+ if (options.get('minor_gridlines')
+ and options['minor_gridlines']['visible']):
+ axis['minor_gridlines'] = \
+ self._get_gridline_properties(options['minor_gridlines'])
+
+ # Only use the first letter of bottom, top, left or right.
+ if axis.get('position'):
+ axis['position'] = axis['position'].lower()[0]
+
+ # Set the position for a category axis on or between the tick marks.
+ if axis.get('position_axis'):
+ if axis['position_axis'] == 'on_tick':
+ axis['position_axis'] = 'midCat'
+ elif axis['position_axis'] == 'between':
+ # Doesn't need to be modified.
+ pass
+ else:
+ # Otherwise use the default value.
+ axis['position_axis'] = None
+
+ # Set the category axis as a date axis.
+ if options.get('date_axis'):
+ self.date_category = True
+
+ # Set the category axis as a text axis.
+ if options.get('text_axis'):
+ self.date_category = False
+ axis['text_axis'] = True
+
+ # Convert datetime args if required.
+ if axis.get('min') and supported_datetime(axis['min']):
+ axis['min'] = datetime_to_excel_datetime(axis['min'],
+ self.date_1904)
+ if axis.get('max') and supported_datetime(axis['max']):
+ axis['max'] = datetime_to_excel_datetime(axis['max'],
+ self.date_1904)
+ if axis.get('crossing') and supported_datetime(axis['crossing']):
+ axis['crossing'] = datetime_to_excel_datetime(axis['crossing'],
+ self.date_1904)
+
+ # Set the font properties if present.
+ axis['num_font'] = self._convert_font_args(options.get('num_font'))
+ axis['name_font'] = self._convert_font_args(options.get('name_font'))
+
+ # Set the axis name layout.
+ axis['name_layout'] = \
+ self._get_layout_properties(options.get('name_layout'), True)
+
+ # Set the line properties for the axis.
+ axis['line'] = Shape._get_line_properties(options.get('line'))
+
+ # Set the fill properties for the axis.
+ axis['fill'] = Shape._get_fill_properties(options.get('fill'))
+
+ # Set the pattern fill properties for the series.
+ axis['pattern'] = Shape._get_pattern_properties(options.get('pattern'))
+
+ # Set the gradient fill properties for the series.
+ axis['gradient'] = \
+ Shape._get_gradient_properties(options.get('gradient'))
+
+ # Pattern fill overrides solid fill.
+ if axis.get('pattern'):
+ axis['fill'] = None
+
+ # Gradient fill overrides the solid and pattern fill.
+ if axis.get('gradient'):
+ axis['pattern'] = None
+ axis['fill'] = None
+
+ # Set the tick marker types.
+ axis['minor_tick_mark'] = \
+ self._get_tick_type(options.get('minor_tick_mark'))
+ axis['major_tick_mark'] = \
+ self._get_tick_type(options.get('major_tick_mark'))
+
+ return axis
+
+ def _convert_font_args(self, options):
+ # Convert user defined font values into private dict values.
+ if not options:
+ return
+
+ font = {
+ 'name': options.get('name'),
+ 'color': options.get('color'),
+ 'size': options.get('size'),
+ 'bold': options.get('bold'),
+ 'italic': options.get('italic'),
+ 'underline': options.get('underline'),
+ 'pitch_family': options.get('pitch_family'),
+ 'charset': options.get('charset'),
+ 'baseline': options.get('baseline', 0),
+ 'rotation': options.get('rotation'),
+ }
+
+ # Convert font size units.
+ if font['size']:
+ font['size'] = int(font['size'] * 100)
+
+ # Convert rotation into 60,000ths of a degree.
+ if font['rotation']:
+ font['rotation'] = 60000 * int(font['rotation'])
+
+ return font
+
+ def _list_to_formula(self, data):
+ # Convert and list of row col values to a range formula.
+
+ # If it isn't an array ref it is probably a formula already.
+ if type(data) is not list:
+ return data
+
+ formula = xl_range_formula(*data)
+
+ return formula
+
+ def _process_names(self, name, name_formula):
+ # Switch name and name_formula parameters if required.
+
+ if name is not None:
+ if isinstance(name, list):
+ # Convert an list of values into a name formula.
+ cell = xl_rowcol_to_cell(name[1], name[2], True, True)
+ name_formula = quote_sheetname(name[0]) + '!' + cell
+ name = ''
+ elif re.match(r'^=?[^!]+!\$?[A-Z]+\$?[0-9]+', name):
+ # Name looks like a formula, use it to set name_formula.
+ name_formula = name
+ name = ''
+
+ return name, name_formula
+
+ def _get_data_type(self, data):
+ # Find the overall type of the data associated with a series.
+
+ # Check for no data in the series.
+ if data is None or len(data) == 0:
+ return 'none'
+
+ if isinstance(data[0], list):
+ return 'multi_str'
+
+ # Determine if data is numeric or strings.
+ for token in data:
+ if token is None:
+ continue
+
+ try:
+ float(token)
+ except ValueError:
+ # Not a number. Assume entire data series is string data.
+ return 'str'
+
+ # The series data was all numeric.
+ return 'num'
+
+ def _get_data_id(self, formula, data):
+ # Assign an id to a each unique series formula or title/axis formula.
+ # Repeated formulas such as for categories get the same id. If the
+ # series or title has user specified data associated with it then
+ # that is also stored. This data is used to populate cached Excel
+ # data when creating a chart. If there is no user defined data then
+ # it will be populated by the parent Workbook._add_chart_data().
+
+ # Ignore series without a range formula.
+ if not formula:
+ return
+
+ # Strip the leading '=' from the formula.
+ if formula.startswith('='):
+ formula = formula.lstrip('=')
+
+ # Store the data id in a hash keyed by the formula and store the data
+ # in a separate array with the same id.
+ if formula not in self.formula_ids:
+ # Haven't seen this formula before.
+ formula_id = len(self.formula_data)
+
+ self.formula_data.append(data)
+ self.formula_ids[formula] = formula_id
+ else:
+ # Formula already seen. Return existing id.
+ formula_id = self.formula_ids[formula]
+
+ # Store user defined data if it isn't already there.
+ if self.formula_data[formula_id] is None:
+ self.formula_data[formula_id] = data
+
+ return formula_id
+
+ def _get_marker_properties(self, marker):
+ # Convert user marker properties to the structure required internally.
+
+ if not marker:
+ return
+
+ # Copy the user defined properties since they will be modified.
+ marker = copy.deepcopy(marker)
+
+ types = {
+ 'automatic': 'automatic',
+ 'none': 'none',
+ 'square': 'square',
+ 'diamond': 'diamond',
+ 'triangle': 'triangle',
+ 'x': 'x',
+ 'star': 'star',
+ 'dot': 'dot',
+ 'short_dash': 'dot',
+ 'dash': 'dash',
+ 'long_dash': 'dash',
+ 'circle': 'circle',
+ 'plus': 'plus',
+ 'picture': 'picture',
+ }
+
+ # Check for valid types.
+ marker_type = marker.get('type')
+
+ if marker_type is not None:
+ if marker_type == 'automatic':
+ marker['automatic'] = 1
+
+ if marker_type in types:
+ marker['type'] = types[marker_type]
+ else:
+ warn("Unknown marker type '%s" % marker_type)
+ return
+
+ # Set the line properties for the marker.
+ line = Shape._get_line_properties(marker.get('line'))
+
+ # Allow 'border' as a synonym for 'line'.
+ if 'border' in marker:
+ line = Shape._get_line_properties(marker['border'])
+
+ # Set the fill properties for the marker.
+ fill = Shape._get_fill_properties(marker.get('fill'))
+
+ # Set the pattern fill properties for the series.
+ pattern = Shape._get_pattern_properties(marker.get('pattern'))
+
+ # Set the gradient fill properties for the series.
+ gradient = Shape._get_gradient_properties(marker.get('gradient'))
+
+ # Pattern fill overrides solid fill.
+ if pattern:
+ self.fill = None
+
+ # Gradient fill overrides the solid and pattern fill.
+ if gradient:
+ pattern = None
+ fill = None
+
+ marker['line'] = line
+ marker['fill'] = fill
+ marker['pattern'] = pattern
+ marker['gradient'] = gradient
+
+ return marker
+
+ def _get_trendline_properties(self, trendline):
+ # Convert user trendline properties to structure required internally.
+
+ if not trendline:
+ return
+
+ # Copy the user defined properties since they will be modified.
+ trendline = copy.deepcopy(trendline)
+
+ types = {
+ 'exponential': 'exp',
+ 'linear': 'linear',
+ 'log': 'log',
+ 'moving_average': 'movingAvg',
+ 'polynomial': 'poly',
+ 'power': 'power',
+ }
+
+ # Check the trendline type.
+ trend_type = trendline.get('type')
+
+ if trend_type in types:
+ trendline['type'] = types[trend_type]
+ else:
+ warn("Unknown trendline type '%s'" % trend_type)
+ return
+
+ # Set the line properties for the trendline.
+ line = Shape._get_line_properties(trendline.get('line'))
+
+ # Allow 'border' as a synonym for 'line'.
+ if 'border' in trendline:
+ line = Shape._get_line_properties(trendline['border'])
+
+ # Set the fill properties for the trendline.
+ fill = Shape._get_fill_properties(trendline.get('fill'))
+
+ # Set the pattern fill properties for the series.
+ pattern = Shape._get_pattern_properties(trendline.get('pattern'))
+
+ # Set the gradient fill properties for the series.
+ gradient = Shape._get_gradient_properties(trendline.get('gradient'))
+
+ # Pattern fill overrides solid fill.
+ if pattern:
+ self.fill = None
+
+ # Gradient fill overrides the solid and pattern fill.
+ if gradient:
+ pattern = None
+ fill = None
+
+ trendline['line'] = line
+ trendline['fill'] = fill
+ trendline['pattern'] = pattern
+ trendline['gradient'] = gradient
+
+ return trendline
+
+ def _get_error_bars_props(self, options):
+ # Convert user error bars properties to structure required internally.
+ if not options:
+ return
+
+ # Default values.
+ error_bars = {
+ 'type': 'fixedVal',
+ 'value': 1,
+ 'endcap': 1,
+ 'direction': 'both'
+ }
+
+ types = {
+ 'fixed': 'fixedVal',
+ 'percentage': 'percentage',
+ 'standard_deviation': 'stdDev',
+ 'standard_error': 'stdErr',
+ 'custom': 'cust',
+ }
+
+ # Check the error bars type.
+ error_type = options['type']
+
+ if error_type in types:
+ error_bars['type'] = types[error_type]
+ else:
+ warn("Unknown error bars type '%s" % error_type)
+ return
+
+ # Set the value for error types that require it.
+ if 'value' in options:
+ error_bars['value'] = options['value']
+
+ # Set the end-cap style.
+ if 'end_style' in options:
+ error_bars['endcap'] = options['end_style']
+
+ # Set the error bar direction.
+ if 'direction' in options:
+ if options['direction'] == 'minus':
+ error_bars['direction'] = 'minus'
+ elif options['direction'] == 'plus':
+ error_bars['direction'] = 'plus'
+ else:
+ # Default to 'both'.
+ pass
+
+ # Set any custom values.
+ error_bars['plus_values'] = options.get('plus_values')
+ error_bars['minus_values'] = options.get('minus_values')
+ error_bars['plus_data'] = options.get('plus_data')
+ error_bars['minus_data'] = options.get('minus_data')
+
+ # Set the line properties for the error bars.
+ error_bars['line'] = Shape._get_line_properties(options.get('line'))
+ error_bars['fill'] = Shape._get_line_properties(options.get('fill'))
+
+ return error_bars
+
+ def _get_gridline_properties(self, options):
+ # Convert user gridline properties to structure required internally.
+
+ # Set the visible property for the gridline.
+ gridline = {'visible': options.get('visible')}
+
+ # Set the line properties for the gridline.
+ gridline['line'] = Shape._get_line_properties(options.get('line'))
+ gridline['fill'] = Shape._get_line_properties(options.get('fill'))
+
+ return gridline
+
+ def _get_labels_properties(self, labels):
+ # Convert user labels properties to the structure required internally.
+
+ if not labels:
+ return None
+
+ # Copy the user defined properties since they will be modified.
+ labels = copy.deepcopy(labels)
+
+ # Map user defined label positions to Excel positions.
+ position = labels.get('position')
+
+ if position:
+ if position in self.label_positions:
+ if position == self.label_position_default:
+ labels['position'] = None
+ else:
+ labels['position'] = self.label_positions[position]
+ else:
+ warn("Unsupported label position '%s' for this chart type"
+ % position)
+ return
+
+ # Map the user defined label separator to the Excel separator.
+ separator = labels.get('separator')
+ separators = {
+ ',': ', ',
+ ';': '; ',
+ '.': '. ',
+ "\n": "\n",
+ ' ': ' ',
+ }
+
+ if separator:
+ if separator in separators:
+ labels['separator'] = separators[separator]
+ else:
+ warn("Unsupported label separator")
+ return
+
+ # Set the font properties if present.
+ labels['font'] = self._convert_font_args(labels.get('font'))
+
+ return labels
+
+ def _get_area_properties(self, options):
+ # Convert user area properties to the structure required internally.
+ area = {}
+
+ # Set the line properties for the chartarea.
+ line = Shape._get_line_properties(options.get('line'))
+
+ # Allow 'border' as a synonym for 'line'.
+ if options.get('border'):
+ line = Shape._get_line_properties(options['border'])
+
+ # Set the fill properties for the chartarea.
+ fill = Shape._get_fill_properties(options.get('fill'))
+
+ # Set the pattern fill properties for the series.
+ pattern = Shape._get_pattern_properties(options.get('pattern'))
+
+ # Set the gradient fill properties for the series.
+ gradient = Shape._get_gradient_properties(options.get('gradient'))
+
+ # Pattern fill overrides solid fill.
+ if pattern:
+ self.fill = None
+
+ # Gradient fill overrides the solid and pattern fill.
+ if gradient:
+ pattern = None
+ fill = None
+
+ # Set the plotarea layout.
+ layout = self._get_layout_properties(options.get('layout'), False)
+
+ area['line'] = line
+ area['fill'] = fill
+ area['pattern'] = pattern
+ area['layout'] = layout
+ area['gradient'] = gradient
+
+ return area
+
+ def _get_layout_properties(self, args, is_text):
+ # Convert user defined layout properties to format used internally.
+ layout = {}
+
+ if not args:
+ return
+
+ if is_text:
+ properties = ('x', 'y')
+ else:
+ properties = ('x', 'y', 'width', 'height')
+
+ # Check for valid properties.
+ for key in args.keys():
+ if key not in properties:
+ warn("Property '%s' allowed not in layout options" % key)
+ return
+
+ # Set the layout properties.
+ for prop in properties:
+ if prop not in args.keys():
+ warn("Property '%s' must be specified in layout options"
+ % prop)
+ return
+
+ value = args[prop]
+
+ try:
+ float(value)
+ except ValueError:
+ warn("Property '%s' value '%s' must be numeric in layout" %
+ (prop, value))
+ return
+
+ if value < 0 or value > 1:
+ warn("Property '%s' value '%s' must be in range "
+ "0 < x <= 1 in layout options" % (prop, value))
+ return
+
+ # Convert to the format used by Excel for easier testing
+ layout[prop] = "%.17g" % value
+
+ return layout
+
+ def _get_points_properties(self, user_points):
+ # Convert user points properties to structure required internally.
+ points = []
+
+ if not user_points:
+ return
+
+ for user_point in user_points:
+ point = {}
+
+ if user_point is not None:
+
+ # Set the line properties for the point.
+ line = Shape._get_line_properties(user_point.get('line'))
+
+ # Allow 'border' as a synonym for 'line'.
+ if 'border' in user_point:
+ line = Shape._get_line_properties(user_point['border'])
+
+ # Set the fill properties for the chartarea.
+ fill = Shape._get_fill_properties(user_point.get('fill'))
+
+ # Set the pattern fill properties for the series.
+ pattern = \
+ Shape._get_pattern_properties(user_point.get('pattern'))
+
+ # Set the gradient fill properties for the series.
+ gradient = \
+ Shape._get_gradient_properties(user_point.get('gradient'))
+
+ # Pattern fill overrides solid fill.
+ if pattern:
+ self.fill = None
+
+ # Gradient fill overrides the solid and pattern fill.
+ if gradient:
+ pattern = None
+ fill = None
+
+ point['line'] = line
+ point['fill'] = fill
+ point['pattern'] = pattern
+ point['gradient'] = gradient
+
+ points.append(point)
+
+ return points
+
+ def _get_display_units(self, display_units):
+ # Convert user defined display units to internal units.
+ if not display_units:
+ return
+
+ types = {
+ 'hundreds': 'hundreds',
+ 'thousands': 'thousands',
+ 'ten_thousands': 'tenThousands',
+ 'hundred_thousands': 'hundredThousands',
+ 'millions': 'millions',
+ 'ten_millions': 'tenMillions',
+ 'hundred_millions': 'hundredMillions',
+ 'billions': 'billions',
+ 'trillions': 'trillions',
+ }
+
+ if display_units in types:
+ display_units = types[display_units]
+ else:
+ warn("Unknown display_units type '%s'" % display_units)
+ return
+
+ return display_units
+
+ def _get_tick_type(self, tick_type):
+ # Convert user defined display units to internal units.
+ if not tick_type:
+ return
+
+ types = {
+ 'outside': 'out',
+ 'inside': 'in',
+ 'none': 'none',
+ 'cross': 'cross',
+ }
+
+ if tick_type in types:
+ tick_type = types[tick_type]
+ else:
+ warn("Unknown tick_type '%s'" % tick_type)
+ return
+
+ return tick_type
+
+ def _get_primary_axes_series(self):
+ # Returns series which use the primary axes.
+ primary_axes_series = []
+
+ for series in self.series:
+ if not series['y2_axis']:
+ primary_axes_series.append(series)
+
+ return primary_axes_series
+
+ def _get_secondary_axes_series(self):
+ # Returns series which use the secondary axes.
+ secondary_axes_series = []
+
+ for series in self.series:
+ if series['y2_axis']:
+ secondary_axes_series.append(series)
+
+ return secondary_axes_series
+
+ def _add_axis_ids(self, args):
+ # Add unique ids for primary or secondary axes
+ chart_id = 5001 + int(self.id)
+ axis_count = 1 + len(self.axis2_ids) + len(self.axis_ids)
+
+ id1 = '%04d%04d' % (chart_id, axis_count)
+ id2 = '%04d%04d' % (chart_id, axis_count + 1)
+
+ if args['primary_axes']:
+ self.axis_ids.append(id1)
+ self.axis_ids.append(id2)
+
+ if not args['primary_axes']:
+ self.axis2_ids.append(id1)
+ self.axis2_ids.append(id2)
+
+ def _set_default_properties(self):
+ # Setup the default properties for a chart.
+
+ self.x_axis['defaults'] = {
+ 'num_format': 'General',
+ 'major_gridlines': {'visible': 0}
+ }
+
+ self.y_axis['defaults'] = {
+ 'num_format': 'General',
+ 'major_gridlines': {'visible': 1}
+ }
+
+ self.x2_axis['defaults'] = {
+ 'num_format': 'General',
+ 'label_position': 'none',
+ 'crossing': 'max',
+ 'visible': 0
+ }
+
+ self.y2_axis['defaults'] = {
+ 'num_format': 'General',
+ 'major_gridlines': {'visible': 0},
+ 'position': 'right',
+ 'visible': 1
+ }
+
+ self.set_x_axis({})
+ self.set_y_axis({})
+
+ self.set_x2_axis({})
+ self.set_y2_axis({})
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_chart_space(self):
+ # Write the element.
+ schema = 'http://schemas.openxmlformats.org/'
+ xmlns_c = schema + 'drawingml/2006/chart'
+ xmlns_a = schema + 'drawingml/2006/main'
+ xmlns_r = schema + 'officeDocument/2006/relationships'
+
+ attributes = [
+ ('xmlns:c', xmlns_c),
+ ('xmlns:a', xmlns_a),
+ ('xmlns:r', xmlns_r),
+ ]
+
+ self._xml_start_tag('c:chartSpace', attributes)
+
+ def _write_lang(self):
+ # Write the element.
+ val = 'en-US'
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:lang', attributes)
+
+ def _write_style(self):
+ # Write the element.
+ style_id = self.style_id
+
+ # Don't write an element for the default style, 2.
+ if style_id == 2:
+ return
+
+ attributes = [('val', style_id)]
+
+ self._xml_empty_tag('c:style', attributes)
+
+ def _write_chart(self):
+ # Write the element.
+ self._xml_start_tag('c:chart')
+
+ if self.title_none:
+ # Turn off the title.
+ self._write_c_auto_title_deleted()
+ else:
+ # Write the chart title elements.
+ if self.title_formula is not None:
+ self._write_title_formula(self.title_formula,
+ self.title_data_id,
+ None,
+ self.title_font,
+ self.title_layout,
+ self.title_overlay)
+ elif self.title_name is not None:
+ self._write_title_rich(self.title_name,
+ None,
+ self.title_font,
+ self.title_layout,
+ self.title_overlay)
+
+ # Write the c:plotArea element.
+ self._write_plot_area()
+
+ # Write the c:legend element.
+ self._write_legend()
+
+ # Write the c:plotVisOnly element.
+ self._write_plot_vis_only()
+
+ # Write the c:dispBlanksAs element.
+ self._write_disp_blanks_as()
+
+ self._xml_end_tag('c:chart')
+
+ def _write_disp_blanks_as(self):
+ # Write the element.
+ val = self.show_blanks
+
+ # Ignore the default value.
+ if val == 'gap':
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:dispBlanksAs', attributes)
+
+ def _write_plot_area(self):
+ # Write the element.
+ self._xml_start_tag('c:plotArea')
+
+ # Write the c:layout element.
+ self._write_layout(self.plotarea.get('layout'), 'plot')
+
+ # Write subclass chart type elements for primary and secondary axes.
+ self._write_chart_type({'primary_axes': True})
+ self._write_chart_type({'primary_axes': False})
+
+ # Configure a combined chart if present.
+ second_chart = self.combined
+ if second_chart:
+ # Secondary axis has unique id otherwise use same as primary.
+ if second_chart.is_secondary:
+ second_chart.id = 1000 + self.id
+ else:
+ second_chart.id = self.id
+
+ # Share the same filehandle for writing.
+ second_chart.fh = self.fh
+
+ # Share series index with primary chart.
+ second_chart.series_index = self.series_index
+
+ # Write the subclass chart type elements for combined chart.
+ second_chart._write_chart_type({'primary_axes': True})
+ second_chart._write_chart_type({'primary_axes': False})
+
+ # Write the category and value elements for the primary axes.
+ args = {'x_axis': self.x_axis,
+ 'y_axis': self.y_axis,
+ 'axis_ids': self.axis_ids}
+
+ if self.date_category:
+ self._write_date_axis(args)
+ else:
+ self._write_cat_axis(args)
+
+ self._write_val_axis(args)
+
+ # Write the category and value elements for the secondary axes.
+ args = {'x_axis': self.x2_axis,
+ 'y_axis': self.y2_axis,
+ 'axis_ids': self.axis2_ids}
+
+ self._write_val_axis(args)
+
+ # Write the secondary axis for the secondary chart.
+ if second_chart and second_chart.is_secondary:
+ args = {'x_axis': second_chart.x2_axis,
+ 'y_axis': second_chart.y2_axis,
+ 'axis_ids': second_chart.axis2_ids}
+
+ second_chart._write_val_axis(args)
+
+ if self.date_category:
+ self._write_date_axis(args)
+ else:
+ self._write_cat_axis(args)
+
+ # Write the c:dTable element.
+ self._write_d_table()
+
+ # Write the c:spPr element for the plotarea formatting.
+ self._write_sp_pr(self.plotarea)
+
+ self._xml_end_tag('c:plotArea')
+
+ def _write_layout(self, layout, layout_type):
+ # Write the element.
+
+ if not layout:
+ # Automatic layout.
+ self._xml_empty_tag('c:layout')
+ else:
+ # User defined manual layout.
+ self._xml_start_tag('c:layout')
+ self._write_manual_layout(layout, layout_type)
+ self._xml_end_tag('c:layout')
+
+ def _write_manual_layout(self, layout, layout_type):
+ # Write the element.
+ self._xml_start_tag('c:manualLayout')
+
+ # Plotarea has a layoutTarget element.
+ if layout_type == 'plot':
+ self._xml_empty_tag('c:layoutTarget', [('val', 'inner')])
+
+ # Set the x, y positions.
+ self._xml_empty_tag('c:xMode', [('val', 'edge')])
+ self._xml_empty_tag('c:yMode', [('val', 'edge')])
+ self._xml_empty_tag('c:x', [('val', layout['x'])])
+ self._xml_empty_tag('c:y', [('val', layout['y'])])
+
+ # For plotarea and legend set the width and height.
+ if layout_type != 'text':
+ self._xml_empty_tag('c:w', [('val', layout['width'])])
+ self._xml_empty_tag('c:h', [('val', layout['height'])])
+
+ self._xml_end_tag('c:manualLayout')
+
+ def _write_chart_type(self, options):
+ # Write the chart type element. This method should be overridden
+ # by the subclasses.
+ return
+
+ def _write_grouping(self, val):
+ # Write the element.
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:grouping', attributes)
+
+ def _write_series(self, series):
+ # Write the series elements.
+ self._write_ser(series)
+
+ def _write_ser(self, series):
+ # Write the element.
+ index = self.series_index
+ self.series_index += 1
+
+ self._xml_start_tag('c:ser')
+
+ # Write the c:idx element.
+ self._write_idx(index)
+
+ # Write the c:order element.
+ self._write_order(index)
+
+ # Write the series name.
+ self._write_series_name(series)
+
+ # Write the c:spPr element.
+ self._write_sp_pr(series)
+
+ # Write the c:marker element.
+ self._write_marker(series['marker'])
+
+ # Write the c:invertIfNegative element.
+ self._write_c_invert_if_negative(series['invert_if_neg'])
+
+ # Write the c:dPt element.
+ self._write_d_pt(series['points'])
+
+ # Write the c:dLbls element.
+ self._write_d_lbls(series['labels'])
+
+ # Write the c:trendline element.
+ self._write_trendline(series['trendline'])
+
+ # Write the c:errBars element.
+ self._write_error_bars(series['error_bars'])
+
+ # Write the c:cat element.
+ self._write_cat(series)
+
+ # Write the c:val element.
+ self._write_val(series)
+
+ # Write the c:smooth element.
+ if self.smooth_allowed:
+ self._write_c_smooth(series['smooth'])
+
+ self._xml_end_tag('c:ser')
+
+ def _write_idx(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:idx', attributes)
+
+ def _write_order(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:order', attributes)
+
+ def _write_series_name(self, series):
+ # Write the series name.
+
+ if series['name_formula'] is not None:
+ self._write_tx_formula(series['name_formula'], series['name_id'])
+ elif series['name'] is not None:
+ self._write_tx_value(series['name'])
+
+ def _write_c_smooth(self, smooth):
+ # Write the element.
+
+ if smooth:
+ self._xml_empty_tag('c:smooth', [('val', '1')])
+
+ def _write_cat(self, series):
+ # Write the element.
+ formula = series['categories']
+ data_id = series['cat_data_id']
+ data = None
+
+ if data_id is not None:
+ data = self.formula_data[data_id]
+
+ # Ignore elements for charts without category values.
+ if not formula:
+ return
+
+ self._xml_start_tag('c:cat')
+
+ # Check the type of cached data.
+ cat_type = self._get_data_type(data)
+
+ if cat_type == 'str':
+ self.cat_has_num_fmt = 0
+ # Write the c:numRef element.
+ self._write_str_ref(formula, data, cat_type)
+
+ elif cat_type == 'multi_str':
+ self.cat_has_num_fmt = 0
+ # Write the c:numRef element.
+ self._write_multi_lvl_str_ref(formula, data)
+
+ else:
+ self.cat_has_num_fmt = 1
+ # Write the c:numRef element.
+ self._write_num_ref(formula, data, cat_type)
+
+ self._xml_end_tag('c:cat')
+
+ def _write_val(self, series):
+ # Write the element.
+ formula = series['values']
+ data_id = series['val_data_id']
+ data = self.formula_data[data_id]
+
+ self._xml_start_tag('c:val')
+
+ # Unlike Cat axes data should only be numeric.
+ # Write the c:numRef element.
+ self._write_num_ref(formula, data, 'num')
+
+ self._xml_end_tag('c:val')
+
+ def _write_num_ref(self, formula, data, ref_type):
+ # Write the element.
+ self._xml_start_tag('c:numRef')
+
+ # Write the c:f element.
+ self._write_series_formula(formula)
+
+ if ref_type == 'num':
+ # Write the c:numCache element.
+ self._write_num_cache(data)
+ elif ref_type == 'str':
+ # Write the c:strCache element.
+ self._write_str_cache(data)
+
+ self._xml_end_tag('c:numRef')
+
+ def _write_str_ref(self, formula, data, ref_type):
+ # Write the element.
+
+ self._xml_start_tag('c:strRef')
+
+ # Write the c:f element.
+ self._write_series_formula(formula)
+
+ if ref_type == 'num':
+ # Write the c:numCache element.
+ self._write_num_cache(data)
+ elif ref_type == 'str':
+ # Write the c:strCache element.
+ self._write_str_cache(data)
+
+ self._xml_end_tag('c:strRef')
+
+ def _write_multi_lvl_str_ref(self, formula, data):
+ # Write the element.
+
+ if not data:
+ return
+
+ self._xml_start_tag('c:multiLvlStrRef')
+
+ # Write the c:f element.
+ self._write_series_formula(formula)
+
+ self._xml_start_tag('c:multiLvlStrCache')
+
+ # Write the c:ptCount element.
+ count = len(data[-1])
+ self._write_pt_count(count)
+
+ for cat_data in reversed(data):
+
+ self._xml_start_tag('c:lvl')
+
+ for i, point in enumerate(cat_data):
+ # Write the c:pt element.
+ self._write_pt(i, cat_data[i])
+
+ self._xml_end_tag('c:lvl')
+
+ self._xml_end_tag('c:multiLvlStrCache')
+ self._xml_end_tag('c:multiLvlStrRef')
+
+ def _write_series_formula(self, formula):
+ # Write the element.
+
+ # Strip the leading '=' from the formula.
+ if formula.startswith('='):
+ formula = formula.lstrip('=')
+
+ self._xml_data_element('c:f', formula)
+
+ def _write_axis_ids(self, args):
+ # Write the elements for the primary or secondary axes.
+
+ # Generate the axis ids.
+ self._add_axis_ids(args)
+
+ if args['primary_axes']:
+ # Write the axis ids for the primary axes.
+ self._write_axis_id(self.axis_ids[0])
+ self._write_axis_id(self.axis_ids[1])
+ else:
+ # Write the axis ids for the secondary axes.
+ self._write_axis_id(self.axis2_ids[0])
+ self._write_axis_id(self.axis2_ids[1])
+
+ def _write_axis_id(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:axId', attributes)
+
+ def _write_cat_axis(self, args):
+ # Write the element. Usually the X axis.
+ x_axis = args['x_axis']
+ y_axis = args['y_axis']
+ axis_ids = args['axis_ids']
+
+ # If there are no axis_ids then we don't need to write this element.
+ if axis_ids is None or not len(axis_ids):
+ return
+
+ position = self.cat_axis_position
+ horiz = self.horiz_cat_axis
+
+ # Overwrite the default axis position with a user supplied value.
+ if x_axis.get('position'):
+ position = x_axis['position']
+
+ self._xml_start_tag('c:catAx')
+
+ self._write_axis_id(axis_ids[0])
+
+ # Write the c:scaling element.
+ self._write_scaling(x_axis.get('reverse'),
+ None,
+ None,
+ None)
+
+ if not x_axis.get('visible'):
+ self._write_delete(1)
+
+ # Write the c:axPos element.
+ self._write_axis_pos(position, y_axis.get('reverse'))
+
+ # Write the c:majorGridlines element.
+ self._write_major_gridlines(x_axis.get('major_gridlines'))
+
+ # Write the c:minorGridlines element.
+ self._write_minor_gridlines(x_axis.get('minor_gridlines'))
+
+ # Write the axis title elements.
+ if x_axis['formula'] is not None:
+ self._write_title_formula(x_axis['formula'],
+ x_axis['data_id'],
+ horiz,
+ x_axis['name_font'],
+ x_axis['name_layout'])
+ elif x_axis['name'] is not None:
+ self._write_title_rich(x_axis['name'],
+ horiz,
+ x_axis['name_font'],
+ x_axis['name_layout'])
+
+ # Write the c:numFmt element.
+ self._write_cat_number_format(x_axis)
+
+ # Write the c:majorTickMark element.
+ self._write_major_tick_mark(x_axis.get('major_tick_mark'))
+
+ # Write the c:minorTickMark element.
+ self._write_minor_tick_mark(x_axis.get('minor_tick_mark'))
+
+ # Write the c:tickLblPos element.
+ self._write_tick_label_pos(x_axis.get('label_position'))
+
+ # Write the c:spPr element for the axis line.
+ self._write_sp_pr(x_axis)
+
+ # Write the axis font elements.
+ self._write_axis_font(x_axis.get('num_font'))
+
+ # Write the c:crossAx element.
+ self._write_cross_axis(axis_ids[1])
+
+ if self.show_crosses or x_axis.get('visible'):
+
+ # Note, the category crossing comes from the value axis.
+ if (y_axis.get('crossing') is None
+ or y_axis.get('crossing') == 'max'):
+
+ # Write the c:crosses element.
+ self._write_crosses(y_axis.get('crossing'))
+ else:
+
+ # Write the c:crossesAt element.
+ self._write_c_crosses_at(y_axis.get('crossing'))
+
+ # Write the c:auto element.
+ if not x_axis.get('text_axis'):
+ self._write_auto(1)
+
+ # Write the c:labelAlign element.
+ self._write_label_align('ctr')
+
+ # Write the c:labelOffset element.
+ self._write_label_offset(100)
+
+ # Write the c:tickLblSkip element.
+ self._write_c_tick_lbl_skip(x_axis.get('interval_unit'))
+
+ # Write the c:tickMarkSkip element.
+ self._write_c_tick_mark_skip(x_axis.get('interval_tick'))
+
+ self._xml_end_tag('c:catAx')
+
+ def _write_val_axis(self, args):
+ # Write the element. Usually the Y axis.
+ x_axis = args['x_axis']
+ y_axis = args['y_axis']
+ axis_ids = args['axis_ids']
+ position = args.get('position', self.val_axis_position)
+ horiz = self.horiz_val_axis
+
+ # If there are no axis_ids then we don't need to write this element.
+ if axis_ids is None or not len(axis_ids):
+ return
+
+ # Overwrite the default axis position with a user supplied value.
+ position = y_axis.get('position') or position
+
+ self._xml_start_tag('c:valAx')
+
+ self._write_axis_id(axis_ids[1])
+
+ # Write the c:scaling element.
+ self._write_scaling(y_axis.get('reverse'),
+ y_axis.get('min'),
+ y_axis.get('max'),
+ y_axis.get('log_base'))
+
+ if not y_axis.get('visible'):
+ self._write_delete(1)
+
+ # Write the c:axPos element.
+ self._write_axis_pos(position, x_axis.get('reverse'))
+
+ # Write the c:majorGridlines element.
+ self._write_major_gridlines(y_axis.get('major_gridlines'))
+
+ # Write the c:minorGridlines element.
+ self._write_minor_gridlines(y_axis.get('minor_gridlines'))
+
+ # Write the axis title elements.
+ if y_axis['formula'] is not None:
+ self._write_title_formula(y_axis['formula'],
+ y_axis['data_id'],
+ horiz,
+ y_axis['name_font'],
+ y_axis['name_layout'])
+ elif y_axis['name'] is not None:
+ self._write_title_rich(y_axis['name'],
+ horiz,
+ y_axis.get('name_font'),
+ y_axis.get('name_layout'))
+
+ # Write the c:numberFormat element.
+ self._write_number_format(y_axis)
+
+ # Write the c:majorTickMark element.
+ self._write_major_tick_mark(y_axis.get('major_tick_mark'))
+
+ # Write the c:minorTickMark element.
+ self._write_minor_tick_mark(y_axis.get('minor_tick_mark'))
+
+ # Write the c:tickLblPos element.
+ self._write_tick_label_pos(y_axis.get('label_position'))
+
+ # Write the c:spPr element for the axis line.
+ self._write_sp_pr(y_axis)
+
+ # Write the axis font elements.
+ self._write_axis_font(y_axis.get('num_font'))
+
+ # Write the c:crossAx element.
+ self._write_cross_axis(axis_ids[0])
+
+ # Note, the category crossing comes from the value axis.
+ if x_axis.get('crossing') is None or x_axis['crossing'] == 'max':
+
+ # Write the c:crosses element.
+ self._write_crosses(x_axis.get('crossing'))
+ else:
+
+ # Write the c:crossesAt element.
+ self._write_c_crosses_at(x_axis.get('crossing'))
+
+ # Write the c:crossBetween element.
+ self._write_cross_between(x_axis.get('position_axis'))
+
+ # Write the c:majorUnit element.
+ self._write_c_major_unit(y_axis.get('major_unit'))
+
+ # Write the c:minorUnit element.
+ self._write_c_minor_unit(y_axis.get('minor_unit'))
+
+ # Write the c:dispUnits element.
+ self._write_disp_units(y_axis.get('display_units'),
+ y_axis.get('display_units_visible'))
+
+ self._xml_end_tag('c:valAx')
+
+ def _write_cat_val_axis(self, args):
+ # Write the element. This is for the second valAx
+ # in scatter plots. Usually the X axis.
+ x_axis = args['x_axis']
+ y_axis = args['y_axis']
+ axis_ids = args['axis_ids']
+ position = args['position'] or self.val_axis_position
+ horiz = self.horiz_val_axis
+
+ # If there are no axis_ids then we don't need to write this element.
+ if axis_ids is None or not len(axis_ids):
+ return
+
+ # Overwrite the default axis position with a user supplied value.
+ position = x_axis.get('position') or position
+
+ self._xml_start_tag('c:valAx')
+
+ self._write_axis_id(axis_ids[0])
+
+ # Write the c:scaling element.
+ self._write_scaling(x_axis.get('reverse'),
+ x_axis.get('min'),
+ x_axis.get('max'),
+ x_axis.get('log_base'))
+
+ if not x_axis.get('visible'):
+ self._write_delete(1)
+
+ # Write the c:axPos element.
+ self._write_axis_pos(position, y_axis.get('reverse'))
+
+ # Write the c:majorGridlines element.
+ self._write_major_gridlines(x_axis.get('major_gridlines'))
+
+ # Write the c:minorGridlines element.
+ self._write_minor_gridlines(x_axis.get('minor_gridlines'))
+
+ # Write the axis title elements.
+ if x_axis['formula'] is not None:
+ self._write_title_formula(x_axis['formula'],
+ x_axis['data_id'],
+ horiz,
+ x_axis['name_font'],
+ x_axis['name_layout'])
+ elif x_axis['name'] is not None:
+ self._write_title_rich(x_axis['name'],
+ horiz,
+ x_axis['name_font'],
+ x_axis['name_layout'])
+
+ # Write the c:numberFormat element.
+ self._write_number_format(x_axis)
+
+ # Write the c:majorTickMark element.
+ self._write_major_tick_mark(x_axis.get('major_tick_mark'))
+
+ # Write the c:minorTickMark element.
+ self._write_minor_tick_mark(x_axis.get('minor_tick_mark'))
+
+ # Write the c:tickLblPos element.
+ self._write_tick_label_pos(x_axis.get('label_position'))
+
+ # Write the c:spPr element for the axis line.
+ self._write_sp_pr(x_axis)
+
+ # Write the axis font elements.
+ self._write_axis_font(x_axis.get('num_font'))
+
+ # Write the c:crossAx element.
+ self._write_cross_axis(axis_ids[1])
+
+ # Note, the category crossing comes from the value axis.
+ if y_axis.get('crossing') is None or y_axis['crossing'] == 'max':
+
+ # Write the c:crosses element.
+ self._write_crosses(y_axis.get('crossing'))
+ else:
+
+ # Write the c:crossesAt element.
+ self._write_c_crosses_at(y_axis.get('crossing'))
+
+ # Write the c:crossBetween element.
+ self._write_cross_between(y_axis.get('position_axis'))
+
+ # Write the c:majorUnit element.
+ self._write_c_major_unit(x_axis.get('major_unit'))
+
+ # Write the c:minorUnit element.
+ self._write_c_minor_unit(x_axis.get('minor_unit'))
+
+ # Write the c:dispUnits element.
+ self._write_disp_units(x_axis.get('display_units'),
+ x_axis.get('display_units_visible'))
+
+ self._xml_end_tag('c:valAx')
+
+ def _write_date_axis(self, args):
+ # Write the element. Usually the X axis.
+ x_axis = args['x_axis']
+ y_axis = args['y_axis']
+ axis_ids = args['axis_ids']
+
+ # If there are no axis_ids then we don't need to write this element.
+ if axis_ids is None or not len(axis_ids):
+ return
+
+ position = self.cat_axis_position
+
+ # Overwrite the default axis position with a user supplied value.
+ position = x_axis.get('position') or position
+
+ self._xml_start_tag('c:dateAx')
+
+ self._write_axis_id(axis_ids[0])
+
+ # Write the c:scaling element.
+ self._write_scaling(x_axis.get('reverse'),
+ x_axis.get('min'),
+ x_axis.get('max'),
+ x_axis.get('log_base'))
+
+ if not x_axis.get('visible'):
+ self._write_delete(1)
+
+ # Write the c:axPos element.
+ self._write_axis_pos(position, y_axis.get('reverse'))
+
+ # Write the c:majorGridlines element.
+ self._write_major_gridlines(x_axis.get('major_gridlines'))
+
+ # Write the c:minorGridlines element.
+ self._write_minor_gridlines(x_axis.get('minor_gridlines'))
+
+ # Write the axis title elements.
+ if x_axis['formula'] is not None:
+ self._write_title_formula(x_axis['formula'],
+ x_axis['data_id'],
+ None,
+ x_axis['name_font'],
+ x_axis['name_layout'])
+ elif x_axis['name'] is not None:
+ self._write_title_rich(x_axis['name'],
+ None,
+ x_axis['name_font'],
+ x_axis['name_layout'])
+
+ # Write the c:numFmt element.
+ self._write_number_format(x_axis)
+
+ # Write the c:majorTickMark element.
+ self._write_major_tick_mark(x_axis.get('major_tick_mark'))
+
+ # Write the c:minorTickMark element.
+ self._write_minor_tick_mark(x_axis.get('minor_tick_mark'))
+
+ # Write the c:tickLblPos element.
+ self._write_tick_label_pos(x_axis.get('label_position'))
+
+ # Write the c:spPr element for the axis line.
+ self._write_sp_pr(x_axis)
+
+ # Write the axis font elements.
+ self._write_axis_font(x_axis.get('num_font'))
+
+ # Write the c:crossAx element.
+ self._write_cross_axis(axis_ids[1])
+
+ if self.show_crosses or x_axis.get('visible'):
+
+ # Note, the category crossing comes from the value axis.
+ if (y_axis.get('crossing') is None
+ or y_axis.get('crossing') == 'max'):
+
+ # Write the c:crosses element.
+ self._write_crosses(y_axis.get('crossing'))
+ else:
+
+ # Write the c:crossesAt element.
+ self._write_c_crosses_at(y_axis.get('crossing'))
+
+ # Write the c:auto element.
+ self._write_auto(1)
+
+ # Write the c:labelOffset element.
+ self._write_label_offset(100)
+
+ # Write the c:tickLblSkip element.
+ self._write_c_tick_lbl_skip(x_axis.get('interval_unit'))
+
+ # Write the c:tickMarkSkip element.
+ self._write_c_tick_mark_skip(x_axis.get('interval_tick'))
+
+ # Write the c:majorUnit element.
+ self._write_c_major_unit(x_axis.get('major_unit'))
+
+ # Write the c:majorTimeUnit element.
+ if x_axis.get('major_unit'):
+ self._write_c_major_time_unit(x_axis['major_unit_type'])
+
+ # Write the c:minorUnit element.
+ self._write_c_minor_unit(x_axis.get('minor_unit'))
+
+ # Write the c:minorTimeUnit element.
+ if x_axis.get('minor_unit'):
+ self._write_c_minor_time_unit(x_axis['minor_unit_type'])
+
+ self._xml_end_tag('c:dateAx')
+
+ def _write_scaling(self, reverse, min_val, max_val, log_base):
+ # Write the element.
+
+ self._xml_start_tag('c:scaling')
+
+ # Write the c:logBase element.
+ self._write_c_log_base(log_base)
+
+ # Write the c:orientation element.
+ self._write_orientation(reverse)
+
+ # Write the c:max element.
+ self._write_c_max(max_val)
+
+ # Write the c:min element.
+ self._write_c_min(min_val)
+
+ self._xml_end_tag('c:scaling')
+
+ def _write_c_log_base(self, val):
+ # Write the element.
+
+ if not val:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:logBase', attributes)
+
+ def _write_orientation(self, reverse):
+ # Write the element.
+ val = 'minMax'
+
+ if reverse:
+ val = 'maxMin'
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:orientation', attributes)
+
+ def _write_c_max(self, max_val):
+ # Write the element.
+
+ if max_val is None:
+ return
+
+ attributes = [('val', max_val)]
+
+ self._xml_empty_tag('c:max', attributes)
+
+ def _write_c_min(self, min_val):
+ # Write the element.
+
+ if min_val is None:
+ return
+
+ attributes = [('val', min_val)]
+
+ self._xml_empty_tag('c:min', attributes)
+
+ def _write_axis_pos(self, val, reverse):
+ # Write the element.
+
+ if reverse:
+ if val == 'l':
+ val = 'r'
+ if val == 'b':
+ val = 't'
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:axPos', attributes)
+
+ def _write_number_format(self, axis):
+ # Write the element. Note: It is assumed that if
+ # a user defined number format is supplied (i.e., non-default) then
+ # the sourceLinked attribute is 0.
+ # The user can override this if required.
+ format_code = axis.get('num_format')
+ source_linked = 1
+
+ # Check if a user defined number format has been set.
+ if (format_code is not None
+ and format_code != axis['defaults']['num_format']):
+ source_linked = 0
+
+ # User override of sourceLinked.
+ if axis.get('num_format_linked'):
+ source_linked = 1
+
+ attributes = [
+ ('formatCode', format_code),
+ ('sourceLinked', source_linked),
+ ]
+
+ self._xml_empty_tag('c:numFmt', attributes)
+
+ def _write_cat_number_format(self, axis):
+ # Write the element. Special case handler for category
+ # axes which don't always have a number format.
+ format_code = axis.get('num_format')
+ source_linked = 1
+ default_format = 1
+
+ # Check if a user defined number format has been set.
+ if (format_code is not None
+ and format_code != axis['defaults']['num_format']):
+ source_linked = 0
+ default_format = 0
+
+ # User override of linkedSource.
+ if axis.get('num_format_linked'):
+ source_linked = 1
+
+ # Skip if cat doesn't have a num format (unless it is non-default).
+ if not self.cat_has_num_fmt and default_format:
+ return
+
+ attributes = [
+ ('formatCode', format_code),
+ ('sourceLinked', source_linked),
+ ]
+
+ self._xml_empty_tag('c:numFmt', attributes)
+
+ def _write_data_label_number_format(self, format_code):
+ # Write the element for data labels.
+ source_linked = 0
+
+ attributes = [
+ ('formatCode', format_code),
+ ('sourceLinked', source_linked),
+ ]
+
+ self._xml_empty_tag('c:numFmt', attributes)
+
+ def _write_major_tick_mark(self, val):
+ # Write the element.
+
+ if not val:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:majorTickMark', attributes)
+
+ def _write_minor_tick_mark(self, val):
+ # Write the element.
+
+ if not val:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:minorTickMark', attributes)
+
+ def _write_tick_label_pos(self, val=None):
+ # Write the element.
+ if val is None or val == 'next_to':
+ val = 'nextTo'
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:tickLblPos', attributes)
+
+ def _write_cross_axis(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:crossAx', attributes)
+
+ def _write_crosses(self, val=None):
+ # Write the element.
+ if val is None:
+ val = 'autoZero'
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:crosses', attributes)
+
+ def _write_c_crosses_at(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:crossesAt', attributes)
+
+ def _write_auto(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:auto', attributes)
+
+ def _write_label_align(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:lblAlgn', attributes)
+
+ def _write_label_offset(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:lblOffset', attributes)
+
+ def _write_c_tick_lbl_skip(self, val):
+ # Write the element.
+ if val is None:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:tickLblSkip', attributes)
+
+ def _write_c_tick_mark_skip(self, val):
+ # Write the element.
+ if val is None:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:tickMarkSkip', attributes)
+
+ def _write_major_gridlines(self, gridlines):
+ # Write the element.
+
+ if not gridlines:
+ return
+
+ if not gridlines['visible']:
+ return
+
+ if gridlines['line']['defined']:
+ self._xml_start_tag('c:majorGridlines')
+
+ # Write the c:spPr element.
+ self._write_sp_pr(gridlines)
+
+ self._xml_end_tag('c:majorGridlines')
+ else:
+ self._xml_empty_tag('c:majorGridlines')
+
+ def _write_minor_gridlines(self, gridlines):
+ # Write the element.
+
+ if not gridlines:
+ return
+
+ if not gridlines['visible']:
+ return
+
+ if gridlines['line']['defined']:
+ self._xml_start_tag('c:minorGridlines')
+
+ # Write the c:spPr element.
+ self._write_sp_pr(gridlines)
+
+ self._xml_end_tag('c:minorGridlines')
+ else:
+ self._xml_empty_tag('c:minorGridlines')
+
+ def _write_cross_between(self, val):
+ # Write the element.
+ if val is None:
+ val = self.cross_between
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:crossBetween', attributes)
+
+ def _write_c_major_unit(self, val):
+ # Write the element.
+
+ if not val:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:majorUnit', attributes)
+
+ def _write_c_minor_unit(self, val):
+ # Write the element.
+
+ if not val:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:minorUnit', attributes)
+
+ def _write_c_major_time_unit(self, val=None):
+ # Write the element.
+ if val is None:
+ val = 'days'
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:majorTimeUnit', attributes)
+
+ def _write_c_minor_time_unit(self, val=None):
+ # Write the element.
+ if val is None:
+ val = 'days'
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:minorTimeUnit', attributes)
+
+ def _write_legend(self):
+ # Write the element.
+ position = self.legend_position
+ font = self.legend_font
+ delete_series = []
+ overlay = 0
+
+ if (self.legend_delete_series is not None
+ and type(self.legend_delete_series) is list):
+ delete_series = self.legend_delete_series
+
+ if position.startswith('overlay_'):
+ position = position.replace('overlay_', '')
+ overlay = 1
+
+ allowed = {
+ 'right': 'r',
+ 'left': 'l',
+ 'top': 't',
+ 'bottom': 'b',
+ }
+
+ if position == 'none':
+ return
+
+ if position not in allowed:
+ return
+
+ position = allowed[position]
+
+ self._xml_start_tag('c:legend')
+
+ # Write the c:legendPos element.
+ self._write_legend_pos(position)
+
+ # Remove series labels from the legend.
+ for index in delete_series:
+ # Write the c:legendEntry element.
+ self._write_legend_entry(index)
+
+ # Write the c:layout element.
+ self._write_layout(self.legend_layout, 'legend')
+
+ if font:
+ self._write_tx_pr(None, font)
+
+ # Write the c:overlay element.
+ if overlay:
+ self._write_overlay()
+
+ self._xml_end_tag('c:legend')
+
+ def _write_legend_pos(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:legendPos', attributes)
+
+ def _write_legend_entry(self, index):
+ # Write the element.
+
+ self._xml_start_tag('c:legendEntry')
+
+ # Write the c:idx element.
+ self._write_idx(index)
+
+ # Write the c:delete element.
+ self._write_delete(1)
+
+ self._xml_end_tag('c:legendEntry')
+
+ def _write_overlay(self):
+ # Write the element.
+ val = 1
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:overlay', attributes)
+
+ def _write_plot_vis_only(self):
+ # Write the element.
+ val = 1
+
+ # Ignore this element if we are plotting hidden data.
+ if self.show_hidden:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:plotVisOnly', attributes)
+
+ def _write_print_settings(self):
+ # Write the element.
+ self._xml_start_tag('c:printSettings')
+
+ # Write the c:headerFooter element.
+ self._write_header_footer()
+
+ # Write the c:pageMargins element.
+ self._write_page_margins()
+
+ # Write the c:pageSetup element.
+ self._write_page_setup()
+
+ self._xml_end_tag('c:printSettings')
+
+ def _write_header_footer(self):
+ # Write the element.
+ self._xml_empty_tag('c:headerFooter')
+
+ def _write_page_margins(self):
+ # Write the element.
+ b = 0.75
+ l = 0.7
+ r = 0.7
+ t = 0.75
+ header = 0.3
+ footer = 0.3
+
+ attributes = [
+ ('b', b),
+ ('l', l),
+ ('r', r),
+ ('t', t),
+ ('header', header),
+ ('footer', footer),
+ ]
+
+ self._xml_empty_tag('c:pageMargins', attributes)
+
+ def _write_page_setup(self):
+ # Write the element.
+ self._xml_empty_tag('c:pageSetup')
+
+ def _write_c_auto_title_deleted(self):
+ # Write the element.
+ self._xml_empty_tag('c:autoTitleDeleted', [('val', 1)])
+
+ def _write_title_rich(self, title, horiz, font, layout, overlay=False):
+ # Write the element for a rich string.
+
+ self._xml_start_tag('c:title')
+
+ # Write the c:tx element.
+ self._write_tx_rich(title, horiz, font)
+
+ # Write the c:layout element.
+ self._write_layout(layout, 'text')
+
+ # Write the c:overlay element.
+ if overlay:
+ self._write_overlay()
+
+ self._xml_end_tag('c:title')
+
+ def _write_title_formula(self, title, data_id, horiz, font, layout,
+ overlay=False):
+ # Write the element for a rich string.
+
+ self._xml_start_tag('c:title')
+
+ # Write the c:tx element.
+ self._write_tx_formula(title, data_id)
+
+ # Write the c:layout element.
+ self._write_layout(layout, 'text')
+
+ # Write the c:overlay element.
+ if overlay:
+ self._write_overlay()
+
+ # Write the c:txPr element.
+ self._write_tx_pr(horiz, font)
+
+ self._xml_end_tag('c:title')
+
+ def _write_tx_rich(self, title, horiz, font):
+ # Write the element.
+
+ self._xml_start_tag('c:tx')
+
+ # Write the c:rich element.
+ self._write_rich(title, horiz, font)
+
+ self._xml_end_tag('c:tx')
+
+ def _write_tx_value(self, title):
+ # Write the element with a value such as for series names.
+
+ self._xml_start_tag('c:tx')
+
+ # Write the c:v element.
+ self._write_v(title)
+
+ self._xml_end_tag('c:tx')
+
+ def _write_tx_formula(self, title, data_id):
+ # Write the element.
+ data = None
+
+ if data_id is not None:
+ data = self.formula_data[data_id]
+
+ self._xml_start_tag('c:tx')
+
+ # Write the c:strRef element.
+ self._write_str_ref(title, data, 'str')
+
+ self._xml_end_tag('c:tx')
+
+ def _write_rich(self, title, horiz, font):
+ # Write the element.
+
+ if font and font.get('rotation'):
+ rotation = font['rotation']
+ else:
+ rotation = None
+
+ self._xml_start_tag('c:rich')
+
+ # Write the a:bodyPr element.
+ self._write_a_body_pr(rotation, horiz)
+
+ # Write the a:lstStyle element.
+ self._write_a_lst_style()
+
+ # Write the a:p element.
+ self._write_a_p_rich(title, font)
+
+ self._xml_end_tag('c:rich')
+
+ def _write_a_body_pr(self, rotation, horiz):
+ # Write the element.
+ attributes = []
+
+ if rotation is None and horiz:
+ rotation = -5400000
+
+ if rotation is not None:
+ attributes.append(('rot', rotation))
+
+ if horiz:
+ attributes.append(('vert', 'horz'))
+
+ self._xml_empty_tag('a:bodyPr', attributes)
+
+ def _write_a_lst_style(self):
+ # Write the element.
+ self._xml_empty_tag('a:lstStyle')
+
+ def _write_a_p_rich(self, title, font):
+ # Write the element for rich string titles.
+
+ self._xml_start_tag('a:p')
+
+ # Write the a:pPr element.
+ self._write_a_p_pr_rich(font)
+
+ # Write the a:r element.
+ self._write_a_r(title, font)
+
+ self._xml_end_tag('a:p')
+
+ def _write_a_p_formula(self, font):
+ # Write the element for formula titles.
+
+ self._xml_start_tag('a:p')
+
+ # Write the a:pPr element.
+ self._write_a_p_pr_formula(font)
+
+ # Write the a:endParaRPr element.
+ self._write_a_end_para_rpr()
+
+ self._xml_end_tag('a:p')
+
+ def _write_a_p_pr_rich(self, font):
+ # Write the element for rich string titles.
+
+ self._xml_start_tag('a:pPr')
+
+ # Write the a:defRPr element.
+ self._write_a_def_rpr(font)
+
+ self._xml_end_tag('a:pPr')
+
+ def _write_a_p_pr_formula(self, font):
+ # Write the element for formula titles.
+
+ self._xml_start_tag('a:pPr')
+
+ # Write the a:defRPr element.
+ self._write_a_def_rpr(font)
+
+ self._xml_end_tag('a:pPr')
+
+ def _write_a_def_rpr(self, font):
+ # Write the element.
+ has_color = 0
+
+ style_attributes = Shape._get_font_style_attributes(font)
+ latin_attributes = Shape._get_font_latin_attributes(font)
+
+ if font and font.get('color') is not None:
+ has_color = 1
+
+ if latin_attributes or has_color:
+ self._xml_start_tag('a:defRPr', style_attributes)
+
+ if has_color:
+ self._write_a_solid_fill({'color': font['color']})
+
+ if latin_attributes:
+ self._write_a_latin(latin_attributes)
+
+ self._xml_end_tag('a:defRPr')
+ else:
+ self._xml_empty_tag('a:defRPr', style_attributes)
+
+ def _write_a_end_para_rpr(self):
+ # Write the element.
+ lang = 'en-US'
+
+ attributes = [('lang', lang)]
+
+ self._xml_empty_tag('a:endParaRPr', attributes)
+
+ def _write_a_r(self, title, font):
+ # Write the element.
+
+ self._xml_start_tag('a:r')
+
+ # Write the a:rPr element.
+ self._write_a_r_pr(font)
+
+ # Write the a:t element.
+ self._write_a_t(title)
+
+ self._xml_end_tag('a:r')
+
+ def _write_a_r_pr(self, font):
+ # Write the element.
+ has_color = 0
+ lang = 'en-US'
+
+ style_attributes = Shape._get_font_style_attributes(font)
+ latin_attributes = Shape._get_font_latin_attributes(font)
+
+ if font and font['color'] is not None:
+ has_color = 1
+
+ # Add the lang type to the attributes.
+ style_attributes.insert(0, ('lang', lang))
+
+ if latin_attributes or has_color:
+ self._xml_start_tag('a:rPr', style_attributes)
+
+ if has_color:
+ self._write_a_solid_fill({'color': font['color']})
+
+ if latin_attributes:
+ self._write_a_latin(latin_attributes)
+
+ self._xml_end_tag('a:rPr')
+ else:
+ self._xml_empty_tag('a:rPr', style_attributes)
+
+ def _write_a_t(self, title):
+ # Write the element.
+
+ self._xml_data_element('a:t', title)
+
+ def _write_tx_pr(self, horiz, font):
+ # Write the element.
+
+ if font and font.get('rotation'):
+ rotation = font['rotation']
+ else:
+ rotation = None
+
+ self._xml_start_tag('c:txPr')
+
+ # Write the a:bodyPr element.
+ self._write_a_body_pr(rotation, horiz)
+
+ # Write the a:lstStyle element.
+ self._write_a_lst_style()
+
+ # Write the a:p element.
+ self._write_a_p_formula(font)
+
+ self._xml_end_tag('c:txPr')
+
+ def _write_marker(self, marker):
+ # Write the element.
+ if marker is None:
+ marker = self.default_marker
+
+ if not marker:
+ return
+ if 'automatic' in marker:
+ return
+
+ self._xml_start_tag('c:marker')
+
+ # Write the c:symbol element.
+ self._write_symbol(marker['type'])
+
+ # Write the c:size element.
+ if marker.get('size'):
+ self._write_marker_size(marker['size'])
+
+ # Write the c:spPr element.
+ self._write_sp_pr(marker)
+
+ self._xml_end_tag('c:marker')
+
+ def _write_marker_value(self):
+ # Write the element without a sub-element.
+ style = self.default_marker
+
+ if not style:
+ return
+
+ attributes = [('val', 1)]
+
+ self._xml_empty_tag('c:marker', attributes)
+
+ def _write_marker_size(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:size', attributes)
+
+ def _write_symbol(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:symbol', attributes)
+
+ def _write_sp_pr(self, series):
+ # Write the element.
+
+ has_fill = False
+ has_line = False
+ has_pattern = series.get('pattern')
+ has_gradient = series.get('gradient')
+
+ if series.get('fill') and series['fill']['defined']:
+ has_fill = True
+
+ if series.get('line') and series['line']['defined']:
+ has_line = True
+
+ if (not has_fill and not has_line and not has_pattern
+ and not has_gradient):
+ return
+
+ self._xml_start_tag('c:spPr')
+
+ # Write the fill elements for solid charts such as pie and bar.
+ if series.get('fill') and series['fill']['defined']:
+ if 'none' in series['fill']:
+ # Write the a:noFill element.
+ self._write_a_no_fill()
+ else:
+ # Write the a:solidFill element.
+ self._write_a_solid_fill(series['fill'])
+
+ if series.get('pattern'):
+ # Write the a:gradFill element.
+ self._write_a_patt_fill(series['pattern'])
+
+ if series.get('gradient'):
+ # Write the a:gradFill element.
+ self._write_a_grad_fill(series['gradient'])
+
+ # Write the a:ln element.
+ if series.get('line') and series['line']['defined']:
+ self._write_a_ln(series['line'])
+
+ self._xml_end_tag('c:spPr')
+
+ def _write_a_ln(self, line):
+ # Write the element.
+ attributes = []
+
+ # Add the line width as an attribute.
+ width = line.get('width')
+
+ if width:
+ # Round width to nearest 0.25, like Excel.
+ width = int((width + 0.125) * 4) / 4.0
+
+ # Convert to internal units.
+ width = int(0.5 + (12700 * width))
+
+ attributes = [('w', width)]
+
+ self._xml_start_tag('a:ln', attributes)
+
+ # Write the line fill.
+ if 'none' in line:
+ # Write the a:noFill element.
+ self._write_a_no_fill()
+ elif 'color' in line:
+ # Write the a:solidFill element.
+ self._write_a_solid_fill(line)
+
+ # Write the line/dash type.
+ line_type = line.get('dash_type')
+ if line_type:
+ # Write the a:prstDash element.
+ self._write_a_prst_dash(line_type)
+
+ self._xml_end_tag('a:ln')
+
+ def _write_a_no_fill(self):
+ # Write the element.
+ self._xml_empty_tag('a:noFill')
+
+ def _write_a_solid_fill(self, fill):
+ # Write the element.
+
+ self._xml_start_tag('a:solidFill')
+
+ if 'color' in fill:
+ color = get_rgb_color(fill['color'])
+ transparency = fill.get('transparency')
+ # Write the a:srgbClr element.
+ self._write_a_srgb_clr(color, transparency)
+
+ self._xml_end_tag('a:solidFill')
+
+ def _write_a_srgb_clr(self, val, transparency=None):
+ # Write the element.
+ attributes = [('val', val)]
+
+ if transparency:
+ self._xml_start_tag('a:srgbClr', attributes)
+
+ # Write the a:alpha element.
+ self._write_a_alpha(transparency)
+
+ self._xml_end_tag('a:srgbClr')
+ else:
+ self._xml_empty_tag('a:srgbClr', attributes)
+
+ def _write_a_alpha(self, val):
+ # Write the element.
+
+ val = int((100 - int(val)) * 1000)
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('a:alpha', attributes)
+
+ def _write_a_prst_dash(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('a:prstDash', attributes)
+
+ def _write_trendline(self, trendline):
+ # Write the element.
+
+ if not trendline:
+ return
+
+ self._xml_start_tag('c:trendline')
+
+ # Write the c:name element.
+ self._write_name(trendline.get('name'))
+
+ # Write the c:spPr element.
+ self._write_sp_pr(trendline)
+
+ # Write the c:trendlineType element.
+ self._write_trendline_type(trendline['type'])
+
+ # Write the c:order element for polynomial trendlines.
+ if trendline['type'] == 'poly':
+ self._write_trendline_order(trendline.get('order'))
+
+ # Write the c:period element for moving average trendlines.
+ if trendline['type'] == 'movingAvg':
+ self._write_period(trendline.get('period'))
+
+ # Write the c:forward element.
+ self._write_forward(trendline.get('forward'))
+
+ # Write the c:backward element.
+ self._write_backward(trendline.get('backward'))
+
+ self._xml_end_tag('c:trendline')
+
+ def _write_trendline_type(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:trendlineType', attributes)
+
+ def _write_name(self, data):
+ # Write the element.
+
+ if data is None:
+ return
+
+ self._xml_data_element('c:name', data)
+
+ def _write_trendline_order(self, val):
+ # Write the element.
+ # val = _[0] is not None ? _[0]: 2
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:order', attributes)
+
+ def _write_period(self, val):
+ # Write the element.
+ # val = _[0] is not None ? _[0]: 2
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:period', attributes)
+
+ def _write_forward(self, val):
+ # Write the element.
+
+ if not val:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:forward', attributes)
+
+ def _write_backward(self, val):
+ # Write the element.
+
+ if not val:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:backward', attributes)
+
+ def _write_hi_low_lines(self):
+ # Write the element.
+ hi_low_lines = self.hi_low_lines
+
+ if hi_low_lines is None:
+ return
+
+ if 'line' in hi_low_lines and hi_low_lines['line']['defined']:
+
+ self._xml_start_tag('c:hiLowLines')
+
+ # Write the c:spPr element.
+ self._write_sp_pr(hi_low_lines)
+
+ self._xml_end_tag('c:hiLowLines')
+ else:
+ self._xml_empty_tag('c:hiLowLines')
+
+ def _write_drop_lines(self):
+ # Write the element.
+ drop_lines = self.drop_lines
+
+ if drop_lines is None:
+ return
+
+ if drop_lines['line']['defined']:
+
+ self._xml_start_tag('c:dropLines')
+
+ # Write the c:spPr element.
+ self._write_sp_pr(drop_lines)
+
+ self._xml_end_tag('c:dropLines')
+ else:
+ self._xml_empty_tag('c:dropLines')
+
+ def _write_overlap(self, val):
+ # Write the element.
+
+ if val is None:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:overlap', attributes)
+
+ def _write_num_cache(self, data):
+ # Write the element.
+ if data:
+ count = len(data)
+ else:
+ count = 0
+
+ self._xml_start_tag('c:numCache')
+
+ # Write the c:formatCode element.
+ self._write_format_code('General')
+
+ # Write the c:ptCount element.
+ self._write_pt_count(count)
+
+ for i in range(count):
+ token = data[i]
+
+ if token is None:
+ continue
+
+ try:
+ float(token)
+ except ValueError:
+ # Write non-numeric data as 0.
+ token = 0
+
+ # Write the c:pt element.
+ self._write_pt(i, token)
+
+ self._xml_end_tag('c:numCache')
+
+ def _write_str_cache(self, data):
+ # Write the element.
+ count = len(data)
+
+ self._xml_start_tag('c:strCache')
+
+ # Write the c:ptCount element.
+ self._write_pt_count(count)
+
+ for i in range(count):
+ # Write the c:pt element.
+ self._write_pt(i, data[i])
+
+ self._xml_end_tag('c:strCache')
+
+ def _write_format_code(self, data):
+ # Write the element.
+
+ self._xml_data_element('c:formatCode', data)
+
+ def _write_pt_count(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:ptCount', attributes)
+
+ def _write_pt(self, idx, value):
+ # Write the element.
+
+ if value is None:
+ return
+
+ attributes = [('idx', idx)]
+
+ self._xml_start_tag('c:pt', attributes)
+
+ # Write the c:v element.
+ self._write_v(value)
+
+ self._xml_end_tag('c:pt')
+
+ def _write_v(self, data):
+ # Write the element.
+
+ self._xml_data_element('c:v', data)
+
+ def _write_protection(self):
+ # Write the element.
+ if not self.protection:
+ return
+
+ self._xml_empty_tag('c:protection')
+
+ def _write_d_pt(self, points):
+ # Write the elements.
+ index = -1
+
+ if not points:
+ return
+
+ for point in points:
+ index += 1
+ if not point:
+ continue
+
+ self._write_d_pt_point(index, point)
+
+ def _write_d_pt_point(self, index, point):
+ # Write an individual element.
+
+ self._xml_start_tag('c:dPt')
+
+ # Write the c:idx element.
+ self._write_idx(index)
+
+ # Write the c:spPr element.
+ self._write_sp_pr(point)
+
+ self._xml_end_tag('c:dPt')
+
+ def _write_d_lbls(self, labels):
+ # Write the element.
+
+ if not labels:
+ return
+
+ self._xml_start_tag('c:dLbls')
+
+ # Write the c:numFmt element.
+ if labels.get('num_format'):
+ self._write_data_label_number_format(labels['num_format'])
+
+ # Write the data label font elements.
+ if labels.get('font'):
+ self._write_axis_font(labels['font'])
+
+ # Write the c:dLblPos element.
+ if labels.get('position'):
+ self._write_d_lbl_pos(labels['position'])
+
+ # Write the c:showLegendKey element.
+ if labels.get('legend_key'):
+ self._write_show_legend_key()
+
+ # Write the c:showVal element.
+ if labels.get('value'):
+ self._write_show_val()
+
+ # Write the c:showCatName element.
+ if labels.get('category'):
+ self._write_show_cat_name()
+
+ # Write the c:showSerName element.
+ if labels.get('series_name'):
+ self._write_show_ser_name()
+
+ # Write the c:showPercent element.
+ if labels.get('percentage'):
+ self._write_show_percent()
+
+ # Write the c:separator element.
+ if labels.get('separator'):
+ self._write_separator(labels['separator'])
+
+ # Write the c:showLeaderLines element.
+ if labels.get('leader_lines'):
+ self._write_show_leader_lines()
+
+ self._xml_end_tag('c:dLbls')
+
+ def _write_show_legend_key(self):
+ # Write the element.
+ val = '1'
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:showLegendKey', attributes)
+
+ def _write_show_val(self):
+ # Write the element.
+ val = 1
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:showVal', attributes)
+
+ def _write_show_cat_name(self):
+ # Write the element.
+ val = 1
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:showCatName', attributes)
+
+ def _write_show_ser_name(self):
+ # Write the element.
+ val = 1
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:showSerName', attributes)
+
+ def _write_show_percent(self):
+ # Write the element.
+ val = 1
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:showPercent', attributes)
+
+ def _write_separator(self, data):
+ # Write the element.
+ self._xml_data_element('c:separator', data)
+
+ def _write_show_leader_lines(self):
+ # Write the element.
+ val = 1
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:showLeaderLines', attributes)
+
+ def _write_d_lbl_pos(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:dLblPos', attributes)
+
+ def _write_delete(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:delete', attributes)
+
+ def _write_c_invert_if_negative(self, invert):
+ # Write the element.
+ val = 1
+
+ if not invert:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:invertIfNegative', attributes)
+
+ def _write_axis_font(self, font):
+ # Write the axis font elements.
+
+ if not font:
+ return
+
+ self._xml_start_tag('c:txPr')
+ self._write_a_body_pr(font.get('rotation'), None)
+ self._write_a_lst_style()
+ self._xml_start_tag('a:p')
+
+ self._write_a_p_pr_rich(font)
+
+ self._write_a_end_para_rpr()
+ self._xml_end_tag('a:p')
+ self._xml_end_tag('c:txPr')
+
+ def _write_a_latin(self, attributes):
+ # Write the element.
+ self._xml_empty_tag('a:latin', attributes)
+
+ def _write_d_table(self):
+ # Write the element.
+ table = self.table
+
+ if not table:
+ return
+
+ self._xml_start_tag('c:dTable')
+
+ if table['horizontal']:
+ # Write the c:showHorzBorder element.
+ self._write_show_horz_border()
+
+ if table['vertical']:
+ # Write the c:showVertBorder element.
+ self._write_show_vert_border()
+
+ if table['outline']:
+ # Write the c:showOutline element.
+ self._write_show_outline()
+
+ if table['show_keys']:
+ # Write the c:showKeys element.
+ self._write_show_keys()
+
+ self._xml_end_tag('c:dTable')
+
+ def _write_show_horz_border(self):
+ # Write the element.
+ attributes = [('val', 1)]
+
+ self._xml_empty_tag('c:showHorzBorder', attributes)
+
+ def _write_show_vert_border(self):
+ # Write the element.
+ attributes = [('val', 1)]
+
+ self._xml_empty_tag('c:showVertBorder', attributes)
+
+ def _write_show_outline(self):
+ # Write the element.
+ attributes = [('val', 1)]
+
+ self._xml_empty_tag('c:showOutline', attributes)
+
+ def _write_show_keys(self):
+ # Write the element.
+ attributes = [('val', 1)]
+
+ self._xml_empty_tag('c:showKeys', attributes)
+
+ def _write_error_bars(self, error_bars):
+ # Write the X and Y error bars.
+
+ if not error_bars:
+ return
+
+ if error_bars['x_error_bars']:
+ self._write_err_bars('x', error_bars['x_error_bars'])
+
+ if error_bars['y_error_bars']:
+ self._write_err_bars('y', error_bars['y_error_bars'])
+
+ def _write_err_bars(self, direction, error_bars):
+ # Write the element.
+
+ if not error_bars:
+ return
+
+ self._xml_start_tag('c:errBars')
+
+ # Write the c:errDir element.
+ self._write_err_dir(direction)
+
+ # Write the c:errBarType element.
+ self._write_err_bar_type(error_bars['direction'])
+
+ # Write the c:errValType element.
+ self._write_err_val_type(error_bars['type'])
+
+ if not error_bars['endcap']:
+ # Write the c:noEndCap element.
+ self._write_no_end_cap()
+
+ if error_bars['type'] == 'stdErr':
+ # Don't need to write a c:errValType tag.
+ pass
+ elif error_bars['type'] == 'cust':
+ # Write the custom error tags.
+ self._write_custom_error(error_bars)
+ else:
+ # Write the c:val element.
+ self._write_error_val(error_bars['value'])
+
+ # Write the c:spPr element.
+ self._write_sp_pr(error_bars)
+
+ self._xml_end_tag('c:errBars')
+
+ def _write_err_dir(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:errDir', attributes)
+
+ def _write_err_bar_type(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:errBarType', attributes)
+
+ def _write_err_val_type(self, val):
+ # Write the element.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:errValType', attributes)
+
+ def _write_no_end_cap(self):
+ # Write the element.
+ attributes = [('val', 1)]
+
+ self._xml_empty_tag('c:noEndCap', attributes)
+
+ def _write_error_val(self, val):
+ # Write the element for error bars.
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:val', attributes)
+
+ def _write_custom_error(self, error_bars):
+ # Write the custom error bars tags.
+
+ if error_bars['plus_values']:
+ # Write the c:plus element.
+ self._xml_start_tag('c:plus')
+
+ if isinstance(error_bars['plus_values'], list):
+ self._write_num_lit(error_bars['plus_values'])
+ else:
+ self._write_num_ref(error_bars['plus_values'],
+ error_bars['plus_data'],
+ 'num')
+ self._xml_end_tag('c:plus')
+
+ if error_bars['minus_values']:
+ # Write the c:minus element.
+ self._xml_start_tag('c:minus')
+
+ if isinstance(error_bars['minus_values'], list):
+ self._write_num_lit(error_bars['minus_values'])
+ else:
+ self._write_num_ref(error_bars['minus_values'],
+ error_bars['minus_data'],
+ 'num')
+ self._xml_end_tag('c:minus')
+
+ def _write_num_lit(self, data):
+ # Write the element for literal number list elements.
+ count = len(data)
+
+ # Write the c:numLit element.
+ self._xml_start_tag('c:numLit')
+
+ # Write the c:formatCode element.
+ self._write_format_code('General')
+
+ # Write the c:ptCount element.
+ self._write_pt_count(count)
+
+ for i in range(count):
+ token = data[i]
+
+ if token is None:
+ continue
+
+ try:
+ float(token)
+ except ValueError:
+ # Write non-numeric data as 0.
+ token = 0
+
+ # Write the c:pt element.
+ self._write_pt(i, token)
+
+ self._xml_end_tag('c:numLit')
+
+ def _write_up_down_bars(self):
+ # Write the element.
+ up_down_bars = self.up_down_bars
+
+ if up_down_bars is None:
+ return
+
+ self._xml_start_tag('c:upDownBars')
+
+ # Write the c:gapWidth element.
+ self._write_gap_width(150)
+
+ # Write the c:upBars element.
+ self._write_up_bars(up_down_bars.get('up'))
+
+ # Write the c:downBars element.
+ self._write_down_bars(up_down_bars.get('down'))
+
+ self._xml_end_tag('c:upDownBars')
+
+ def _write_gap_width(self, val):
+ # Write the element.
+
+ if val is None:
+ return
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:gapWidth', attributes)
+
+ def _write_up_bars(self, bar_format):
+ # Write the element.
+
+ if bar_format['line'] and bar_format['line']['defined']:
+ self._xml_start_tag('c:upBars')
+
+ # Write the c:spPr element.
+ self._write_sp_pr(bar_format)
+
+ self._xml_end_tag('c:upBars')
+ else:
+ self._xml_empty_tag('c:upBars')
+
+ def _write_down_bars(self, bar_format):
+ # Write the element.
+
+ if bar_format['line'] and bar_format['line']['defined']:
+ self._xml_start_tag('c:downBars')
+
+ # Write the c:spPr element.
+ self._write_sp_pr(bar_format)
+
+ self._xml_end_tag('c:downBars')
+ else:
+ self._xml_empty_tag('c:downBars')
+
+ def _write_disp_units(self, units, display):
+ # Write the element.
+
+ if not units:
+ return
+
+ attributes = [('val', units)]
+
+ self._xml_start_tag('c:dispUnits')
+ self._xml_empty_tag('c:builtInUnit', attributes)
+
+ if display:
+ self._xml_start_tag('c:dispUnitsLbl')
+ self._xml_empty_tag('c:layout')
+ self._xml_end_tag('c:dispUnitsLbl')
+
+ self._xml_end_tag('c:dispUnits')
+
+ def _write_a_grad_fill(self, gradient):
+ # Write the element.
+
+ attributes = [('flip', 'none'), ('rotWithShape', '1')]
+
+ if gradient['type'] == 'linear':
+ attributes = []
+
+ self._xml_start_tag('a:gradFill', attributes)
+
+ # Write the a:gsLst element.
+ self._write_a_gs_lst(gradient)
+
+ if gradient['type'] == 'linear':
+ # Write the a:lin element.
+ self._write_a_lin(gradient['angle'])
+ else:
+ # Write the a:path element.
+ self._write_a_path(gradient['type'])
+
+ # Write the a:tileRect element.
+ self._write_a_tile_rect(gradient['type'])
+
+ self._xml_end_tag('a:gradFill')
+
+ def _write_a_gs_lst(self, gradient):
+ # Write the element.
+ positions = gradient['positions']
+ colors = gradient['colors']
+
+ self._xml_start_tag('a:gsLst')
+
+ for i in range(len(colors)):
+ pos = int(positions[i] * 1000)
+ attributes = [('pos', pos)]
+ self._xml_start_tag('a:gs', attributes)
+
+ # Write the a:srgbClr element.
+ # TODO: Wait for a feature request to support transparency.
+ color = get_rgb_color(colors[i])
+ self._write_a_srgb_clr(color)
+
+ self._xml_end_tag('a:gs')
+
+ self._xml_end_tag('a:gsLst')
+
+ def _write_a_lin(self, angle):
+ # Write the element.
+
+ angle = int(60000 * angle)
+
+ attributes = [
+ ('ang', angle),
+ ('scaled', '0'),
+ ]
+
+ self._xml_empty_tag('a:lin', attributes)
+
+ def _write_a_path(self, gradient_type):
+ # Write the element.
+
+ attributes = [('path', gradient_type)]
+
+ self._xml_start_tag('a:path', attributes)
+
+ # Write the a:fillToRect element.
+ self._write_a_fill_to_rect(gradient_type)
+
+ self._xml_end_tag('a:path')
+
+ def _write_a_fill_to_rect(self, gradient_type):
+ # Write the element.
+
+ l = '100000'
+ t = '100000'
+
+ if gradient_type == 'shape':
+ attributes = [
+ ('l', '50000'),
+ ('t', '50000'),
+ ('r', '50000'),
+ ('b', '50000'),
+ ]
+ else:
+ attributes = [
+ ('l', '100000'),
+ ('t', '100000'),
+ ]
+
+ self._xml_empty_tag('a:fillToRect', attributes)
+
+ def _write_a_tile_rect(self, gradient_type):
+ # Write the element.
+
+ if gradient_type == 'shape':
+ attributes = []
+ else:
+ attributes = [
+ ('r', '-100000'),
+ ('b', '-100000'),
+ ]
+
+ self._xml_empty_tag('a:tileRect', attributes)
+
+ def _write_a_patt_fill(self, pattern):
+ # Write the element.
+
+ attributes = [('prst', pattern['pattern'])]
+
+ self._xml_start_tag('a:pattFill', attributes)
+
+ # Write the a:fgClr element.
+ self._write_a_fg_clr(pattern['fg_color'])
+
+ # Write the a:bgClr element.
+ self._write_a_bg_clr(pattern['bg_color'])
+
+ self._xml_end_tag('a:pattFill')
+
+ def _write_a_fg_clr(self, color):
+ # Write the element.
+
+ color = get_rgb_color(color)
+
+ self._xml_start_tag('a:fgClr')
+
+ # Write the a:srgbClr element.
+ self._write_a_srgb_clr(color)
+
+ self._xml_end_tag('a:fgClr')
+
+ def _write_a_bg_clr(self, color):
+ # Write the element.
+
+ color = get_rgb_color(color)
+
+ self._xml_start_tag('a:bgClr')
+
+ # Write the a:srgbClr element.
+ self._write_a_srgb_clr(color)
+
+ self._xml_end_tag('a:bgClr')
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_area.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_area.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,103 @@
+###############################################################################
+#
+# ChartArea - A class for writing the Excel XLSX Area charts.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+from . import chart
+
+
+class ChartArea(chart.Chart):
+ """
+ A class for writing the Excel XLSX Area charts.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self, options=None):
+ """
+ Constructor.
+
+ """
+ super(ChartArea, self).__init__()
+
+ if options is None:
+ options = {}
+
+ self.subtype = options.get('subtype')
+
+ if not self.subtype:
+ self.subtype = 'standard'
+
+ self.cross_between = 'midCat'
+ self.show_crosses = 0
+
+ # Override and reset the default axis values.
+ if self.subtype == 'percent_stacked':
+ self.y_axis['defaults']['num_format'] = '0%'
+
+ # Set the available data label positions for this chart type.
+ self.label_position_default = 'center'
+ self.label_positions = {'center': 'ctr'}
+
+ self.set_y_axis({})
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _write_chart_type(self, args):
+ # Override the virtual superclass method with a chart specific method.
+ # Write the c:areaChart element.
+ self._write_area_chart(args)
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+ #
+ def _write_area_chart(self, args):
+ # Write the element.
+
+ if args['primary_axes']:
+ series = self._get_primary_axes_series()
+ else:
+ series = self._get_secondary_axes_series()
+
+ if not len(series):
+ return
+
+ subtype = self.subtype
+
+ if subtype == 'percent_stacked':
+ subtype = 'percentStacked'
+
+ self._xml_start_tag('c:areaChart')
+
+ # Write the c:grouping element.
+ self._write_grouping(subtype)
+
+ # Write the series elements.
+ for data in series:
+ self._write_ser(data)
+
+ # Write the c:dropLines element.
+ self._write_drop_lines()
+
+ # Write the c:marker element.
+ self._write_marker_value()
+
+ # Write the c:axId elements
+ self._write_axis_ids(args)
+
+ self._xml_end_tag('c:areaChart')
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_area.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_area.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_bar.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_bar.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,175 @@
+###############################################################################
+#
+# ChartBar - A class for writing the Excel XLSX Bar charts.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+from . import chart
+from warnings import warn
+
+
+class ChartBar(chart.Chart):
+ """
+ A class for writing the Excel XLSX Bar charts.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self, options=None):
+ """
+ Constructor.
+
+ """
+ super(ChartBar, self).__init__()
+
+ if options is None:
+ options = {}
+
+ self.subtype = options.get('subtype')
+
+ if not self.subtype:
+ self.subtype = 'clustered'
+
+ self.cat_axis_position = 'l'
+ self.val_axis_position = 'b'
+ self.horiz_val_axis = 0
+ self.horiz_cat_axis = 1
+ self.show_crosses = 0
+
+ # Override and reset the default axis values.
+ self.x_axis['defaults']['major_gridlines'] = {'visible': 1}
+ self.y_axis['defaults']['major_gridlines'] = {'visible': 0}
+
+ if self.subtype == 'percent_stacked':
+ self.x_axis['defaults']['num_format'] = '0%'
+
+ # Set the available data label positions for this chart type.
+ self.label_position_default = 'outside_end'
+ self.label_positions = {
+ 'center': 'ctr',
+ 'inside_base': 'inBase',
+ 'inside_end': 'inEnd',
+ 'outside_end': 'outEnd'}
+
+ self.set_x_axis({})
+ self.set_y_axis({})
+
+ def combine(self, chart=None):
+ """
+ Create a combination chart with a secondary chart.
+
+ Note: Override parent method to add an extra check that is required
+ for Bar charts to ensure that their combined chart is on a secondary
+ axis.
+
+ Args:
+ chart: The secondary chart to combine with the primary chart.
+
+ Returns:
+ Nothing.
+
+ """
+ if chart is None:
+ return
+
+ if not chart.is_secondary:
+ warn('Charts combined with Bar charts must be on a secondary axis')
+
+ self.combined = chart
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _write_chart_type(self, args):
+ # Override the virtual superclass method with a chart specific method.
+ if args['primary_axes']:
+ # Reverse X and Y axes for Bar charts.
+ tmp = self.y_axis
+ self.y_axis = self.x_axis
+ self.x_axis = tmp
+
+ if self.y2_axis['position'] == 'r':
+ self.y2_axis['position'] = 't'
+
+ # Write the c:barChart element.
+ self._write_bar_chart(args)
+
+ def _write_bar_chart(self, args):
+ # Write the element.
+
+ if args['primary_axes']:
+ series = self._get_primary_axes_series()
+ else:
+ series = self._get_secondary_axes_series()
+
+ if not len(series):
+ return
+
+ subtype = self.subtype
+ if subtype == 'percent_stacked':
+ subtype = 'percentStacked'
+
+ # Set a default overlap for stacked charts.
+ if 'stacked' in self.subtype:
+ if self.series_overlap_1 is None:
+ self.series_overlap_1 = 100
+
+ self._xml_start_tag('c:barChart')
+
+ # Write the c:barDir element.
+ self._write_bar_dir()
+
+ # Write the c:grouping element.
+ self._write_grouping(subtype)
+
+ # Write the c:ser elements.
+ for data in series:
+ self._write_ser(data)
+
+ # Write the c:marker element.
+ self._write_marker_value()
+
+ # Write the c:gapWidth element.
+ if args['primary_axes']:
+ self._write_gap_width(self.series_gap_1)
+ else:
+ self._write_gap_width(self.series_gap_2)
+
+ # Write the c:overlap element.
+ if args['primary_axes']:
+ self._write_overlap(self.series_overlap_1)
+ else:
+ self._write_overlap(self.series_overlap_2)
+
+ # Write the c:axId elements
+ self._write_axis_ids(args)
+
+ self._xml_end_tag('c:barChart')
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_bar_dir(self):
+ # Write the element.
+ val = 'bar'
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:barDir', attributes)
+
+ def _write_err_dir(self, val):
+ # Overridden from Chart class since it is not used in Bar charts.
+ pass
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_bar.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_bar.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_column.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_column.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,134 @@
+###############################################################################
+#
+# ChartColumn - A class for writing the Excel XLSX Column charts.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+from . import chart
+
+
+class ChartColumn(chart.Chart):
+ """
+ A class for writing the Excel XLSX Column charts.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self, options=None):
+ """
+ Constructor.
+
+ """
+ super(ChartColumn, self).__init__()
+
+ if options is None:
+ options = {}
+
+ self.subtype = options.get('subtype')
+
+ if not self.subtype:
+ self.subtype = 'clustered'
+
+ self.horiz_val_axis = 0
+
+ if self.subtype == 'percent_stacked':
+ self.y_axis['defaults']['num_format'] = '0%'
+
+ # Set the available data label positions for this chart type.
+ self.label_position_default = 'outside_end'
+ self.label_positions = {
+ 'center': 'ctr',
+ 'inside_base': 'inBase',
+ 'inside_end': 'inEnd',
+ 'outside_end': 'outEnd'}
+
+ self.set_y_axis({})
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _write_chart_type(self, args):
+ # Override the virtual superclass method with a chart specific method.
+
+ # Write the c:barChart element.
+ self._write_bar_chart(args)
+
+ def _write_bar_chart(self, args):
+ # Write the element.
+
+ if args['primary_axes']:
+ series = self._get_primary_axes_series()
+ else:
+ series = self._get_secondary_axes_series()
+
+ if not len(series):
+ return
+
+ subtype = self.subtype
+ if subtype == 'percent_stacked':
+ subtype = 'percentStacked'
+
+ # Set a default overlap for stacked charts.
+ if 'stacked' in self.subtype:
+ if self.series_overlap_1 is None:
+ self.series_overlap_1 = 100
+
+ self._xml_start_tag('c:barChart')
+
+ # Write the c:barDir element.
+ self._write_bar_dir()
+
+ # Write the c:grouping element.
+ self._write_grouping(subtype)
+
+ # Write the c:ser elements.
+ for data in series:
+ self._write_ser(data)
+
+ # Write the c:marker element.
+ self._write_marker_value()
+
+ # Write the c:gapWidth element.
+ if args['primary_axes']:
+ self._write_gap_width(self.series_gap_1)
+ else:
+ self._write_gap_width(self.series_gap_2)
+
+ # Write the c:overlap element.
+ if args['primary_axes']:
+ self._write_overlap(self.series_overlap_1)
+ else:
+ self._write_overlap(self.series_overlap_2)
+
+ # Write the c:axId elements
+ self._write_axis_ids(args)
+
+ self._xml_end_tag('c:barChart')
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_bar_dir(self):
+ # Write the element.
+ val = 'col'
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:barDir', attributes)
+
+ def _write_err_dir(self, val):
+ # Overridden from Chart class since it is not used in Column charts.
+ pass
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_column.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_column.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_doughnut.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_doughnut.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,102 @@
+###############################################################################
+#
+# ChartDoughnut - A class for writing the Excel XLSX Doughnut charts.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+from warnings import warn
+from . import chart_pie
+
+
+class ChartDoughnut(chart_pie.ChartPie):
+ """
+ A class for writing the Excel XLSX Doughnut charts.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self, options=None):
+ """
+ Constructor.
+
+ """
+ super(ChartDoughnut, self).__init__()
+
+ if options is None:
+ options = {}
+
+ self.vary_data_color = 1
+ self.rotation = 0
+ self.hole_size = 50
+
+ def set_hole_size(self, size):
+ """
+ Set the Doughnut chart hole size.
+
+ Args:
+ size: 10 <= size <= 90.
+
+ Returns:
+ Nothing.
+
+ """
+ if size is None:
+ return
+
+ # Ensure the size is in Excel's range.
+ if size < 10 or size > 90:
+ warn("Chart hole size %d outside Excel range: 10 <= size <= 90"
+ % size)
+ return
+
+ self.hole_size = int(size)
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _write_chart_type(self, args):
+ # Override the virtual superclass method with a chart specific method.
+ # Write the c:doughnutChart element.
+ self._write_doughnut_chart(args)
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_doughnut_chart(self, args):
+ # Write the element. Over-ridden method to remove
+ # axis_id code since Doughnut charts don't require val and cat axes.
+ self._xml_start_tag('c:doughnutChart')
+
+ # Write the c:varyColors element.
+ self._write_vary_colors()
+
+ # Write the series elements.
+ for data in self.series:
+ self._write_ser(data)
+
+ # Write the c:firstSliceAng element.
+ self._write_first_slice_ang()
+
+ # Write the c:holeSize element.
+ self._write_c_hole_size()
+
+ self._xml_end_tag('c:doughnutChart')
+
+ def _write_c_hole_size(self):
+ # Write the element.
+ attributes = [('val', self.hole_size)]
+
+ self._xml_empty_tag('c:holeSize', attributes)
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_doughnut.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_doughnut.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_line.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_line.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,119 @@
+###############################################################################
+#
+# ChartLine - A class for writing the Excel XLSX Line charts.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+from . import chart
+
+
+class ChartLine(chart.Chart):
+ """
+ A class for writing the Excel XLSX Line charts.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self, options=None):
+ """
+ Constructor.
+
+ """
+ super(ChartLine, self).__init__()
+
+ if options is None:
+ options = {}
+
+ self.default_marker = {'type': 'none'}
+ self.smooth_allowed = True
+
+ # Set the available data label positions for this chart type.
+ self.label_position_default = 'right'
+ self.label_positions = {
+ 'center': 'ctr',
+ 'right': 'r',
+ 'left': 'l',
+ 'above': 't',
+ 'below': 'b',
+ # For backward compatibility.
+ 'top': 't',
+ 'bottom': 'b'}
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _write_chart_type(self, args):
+ # Override the virtual superclass method with a chart specific method.
+ # Write the c:lineChart element.
+ self._write_line_chart(args)
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_line_chart(self, args):
+ # Write the element.
+
+ if args['primary_axes']:
+ series = self._get_primary_axes_series()
+ else:
+ series = self._get_secondary_axes_series()
+
+ if not len(series):
+ return
+
+ self._xml_start_tag('c:lineChart')
+
+ # Write the c:grouping element.
+ self._write_grouping('standard')
+
+ # Write the series elements.
+ for data in series:
+ self._write_ser(data)
+
+ # Write the c:dropLines element.
+ self._write_drop_lines()
+
+ # Write the c:hiLowLines element.
+ self._write_hi_low_lines()
+
+ # Write the c:upDownBars element.
+ self._write_up_down_bars()
+
+ # Write the c:marker element.
+ self._write_marker_value()
+
+ # Write the c:axId elements
+ self._write_axis_ids(args)
+
+ self._xml_end_tag('c:lineChart')
+
+ def _write_d_pt_point(self, index, point):
+ # Write an individual element. Override the parent method to
+ # add markers.
+
+ self._xml_start_tag('c:dPt')
+
+ # Write the c:idx element.
+ self._write_idx(index)
+
+ self._xml_start_tag('c:marker')
+
+ # Write the c:spPr element.
+ self._write_sp_pr(point)
+
+ self._xml_end_tag('c:marker')
+
+ self._xml_end_tag('c:dPt')
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_line.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_line.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_pie.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_pie.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,227 @@
+###############################################################################
+#
+# ChartPie - A class for writing the Excel XLSX Pie charts.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+from warnings import warn
+from . import chart
+
+
+class ChartPie(chart.Chart):
+ """
+ A class for writing the Excel XLSX Pie charts.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self, options=None):
+ """
+ Constructor.
+
+ """
+ super(ChartPie, self).__init__()
+
+ if options is None:
+ options = {}
+
+ self.vary_data_color = 1
+ self.rotation = 0
+
+ # Set the available data label positions for this chart type.
+ self.label_position_default = 'best_fit'
+ self.label_positions = {
+ 'center': 'ctr',
+ 'inside_end': 'inEnd',
+ 'outside_end': 'outEnd',
+ 'best_fit': 'bestFit'}
+
+ def set_rotation(self, rotation):
+ """
+ Set the Pie/Doughnut chart rotation: the angle of the first slice.
+
+ Args:
+ rotation: First segment angle: 0 <= rotation <= 360.
+
+ Returns:
+ Nothing.
+
+ """
+ if rotation is None:
+ return
+
+ # Ensure the rotation is in Excel's range.
+ if rotation < 0 or rotation > 360:
+ warn("Chart rotation %d outside Excel range: 0 <= rotation <= 360"
+ % rotation)
+ return
+
+ self.rotation = int(rotation)
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _write_chart_type(self, args):
+ # Override the virtual superclass method with a chart specific method.
+ # Write the c:pieChart element.
+ self._write_pie_chart(args)
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_pie_chart(self, args):
+ # Write the element. Over-ridden method to remove
+ # axis_id code since Pie charts don't require val and cat axes.
+ self._xml_start_tag('c:pieChart')
+
+ # Write the c:varyColors element.
+ self._write_vary_colors()
+
+ # Write the series elements.
+ for data in self.series:
+ self._write_ser(data)
+
+ # Write the c:firstSliceAng element.
+ self._write_first_slice_ang()
+
+ self._xml_end_tag('c:pieChart')
+
+ def _write_plot_area(self):
+ # Over-ridden method to remove the cat_axis() and val_axis() code
+ # since Pie charts don't require those axes.
+ #
+ # Write the element.
+
+ self._xml_start_tag('c:plotArea')
+
+ # Write the c:layout element.
+ self._write_layout(self.plotarea.get('layout'), 'plot')
+
+ # Write the subclass chart type element.
+ self._write_chart_type(None)
+
+ self._xml_end_tag('c:plotArea')
+
+ def _write_legend(self):
+ # Over-ridden method to add to legend.
+ # Write the element.
+
+ position = self.legend_position
+ font = self.legend_font
+ delete_series = []
+ overlay = 0
+
+ if (self.legend_delete_series is not None
+ and type(self.legend_delete_series) is list):
+ delete_series = self.legend_delete_series
+
+ if position.startswith('overlay_'):
+ position = position.replace('overlay_', '')
+ overlay = 1
+
+ allowed = {
+ 'right': 'r',
+ 'left': 'l',
+ 'top': 't',
+ 'bottom': 'b',
+ }
+
+ if position == 'none':
+ return
+
+ if position not in allowed:
+ return
+
+ position = allowed[position]
+
+ self._xml_start_tag('c:legend')
+
+ # Write the c:legendPos element.
+ self._write_legend_pos(position)
+
+ # Remove series labels from the legend.
+ for index in delete_series:
+ # Write the c:legendEntry element.
+ self._write_legend_entry(index)
+
+ # Write the c:layout element.
+ self._write_layout(self.legend_layout, 'legend')
+
+ # Write the c:overlay element.
+ if overlay:
+ self._write_overlay()
+
+ # Write the c:txPr element. Over-ridden.
+ self._write_tx_pr_legend(None, font)
+
+ self._xml_end_tag('c:legend')
+
+ def _write_tx_pr_legend(self, horiz, font):
+ # Write the element for legends.
+
+ if font and font.get('rotation'):
+ rotation = font['rotation']
+ else:
+ rotation = None
+
+ self._xml_start_tag('c:txPr')
+
+ # Write the a:bodyPr element.
+ self._write_a_body_pr(rotation, horiz)
+
+ # Write the a:lstStyle element.
+ self._write_a_lst_style()
+
+ # Write the a:p element.
+ self._write_a_p_legend(font)
+
+ self._xml_end_tag('c:txPr')
+
+ def _write_a_p_legend(self, font):
+ # Write the element for legends.
+
+ self._xml_start_tag('a:p')
+
+ # Write the a:pPr element.
+ self._write_a_p_pr_legend(font)
+
+ # Write the a:endParaRPr element.
+ self._write_a_end_para_rpr()
+
+ self._xml_end_tag('a:p')
+
+ def _write_a_p_pr_legend(self, font):
+ # Write the element for legends.
+ attributes = [('rtl', 0)]
+
+ self._xml_start_tag('a:pPr', attributes)
+
+ # Write the a:defRPr element.
+ self._write_a_def_rpr(font)
+
+ self._xml_end_tag('a:pPr')
+
+ def _write_vary_colors(self):
+ # Write the element.
+ attributes = [('val', 1)]
+
+ self._xml_empty_tag('c:varyColors', attributes)
+
+ def _write_first_slice_ang(self):
+ # Write the element.
+ attributes = [('val', self.rotation)]
+
+ self._xml_empty_tag('c:firstSliceAng', attributes)
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_pie.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_pie.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_radar.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_radar.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,101 @@
+###############################################################################
+#
+# ChartRadar - A class for writing the Excel XLSX Radar charts.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+from . import chart
+
+
+class ChartRadar(chart.Chart):
+ """
+ A class for writing the Excel XLSX Radar charts.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self, options=None):
+ """
+ Constructor.
+
+ """
+ super(ChartRadar, self).__init__()
+
+ if options is None:
+ options = {}
+
+ self.subtype = options.get('subtype')
+
+ if not self.subtype:
+ self.subtype = 'marker'
+ self.default_marker = {'type': 'none'}
+
+ # Override and reset the default axis values.
+ self.x_axis['defaults']['major_gridlines'] = {'visible': 1}
+ self.set_x_axis({})
+
+ # Set the available data label positions for this chart type.
+ self.label_position_default = 'center'
+ self.label_positions = {'center': 'ctr'}
+
+ # Hardcode major_tick_mark for now until there is an accessor.
+ self.y_axis['major_tick_mark'] = 'cross'
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _write_chart_type(self, args):
+ # Write the c:radarChart element.
+ self._write_radar_chart(args)
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_radar_chart(self, args):
+ # Write the element.
+
+ if args['primary_axes']:
+ series = self._get_primary_axes_series()
+ else:
+ series = self._get_secondary_axes_series()
+
+ if not len(series):
+ return
+
+ self._xml_start_tag('c:radarChart')
+
+ # Write the c:radarStyle element.
+ self._write_radar_style()
+
+ # Write the series elements.
+ for data in series:
+ self._write_ser(data)
+
+ # Write the c:axId elements
+ self._write_axis_ids(args)
+
+ self._xml_end_tag('c:radarChart')
+
+ def _write_radar_style(self):
+ # Write the element.
+ val = 'marker'
+
+ if self.subtype == 'filled':
+ val = 'filled'
+
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:radarStyle', attributes)
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_radar.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_radar.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_scatter.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_scatter.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,327 @@
+###############################################################################
+#
+# ChartScatter - A class for writing the Excel XLSX Scatter charts.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+from . import chart
+
+
+class ChartScatter(chart.Chart):
+ """
+ A class for writing the Excel XLSX Scatter charts.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self, options=None):
+ """
+ Constructor.
+
+ """
+ super(ChartScatter, self).__init__()
+
+ if options is None:
+ options = {}
+
+ self.subtype = options.get('subtype')
+
+ if not self.subtype:
+ self.subtype = 'marker_only'
+
+ self.cross_between = 'midCat'
+ self.horiz_val_axis = 0
+ self.val_axis_position = 'b'
+ self.smooth_allowed = True
+ self.requires_category = True
+
+ # Set the available data label positions for this chart type.
+ self.label_position_default = 'right'
+ self.label_positions = {
+ 'center': 'ctr',
+ 'right': 'r',
+ 'left': 'l',
+ 'above': 't',
+ 'below': 'b',
+ # For backward compatibility.
+ 'top': 't',
+ 'bottom': 'b'}
+
+ def combine(self, chart=None):
+ """
+ Create a combination chart with a secondary chart.
+
+ Note: Override parent method to add a warning.
+
+ Args:
+ chart: The secondary chart to combine with the primary chart.
+
+ Returns:
+ Nothing.
+
+ """
+ if chart is None:
+ return
+
+ warn('Combined chart not currently supported with scatter chart '
+ 'as the primary chart')
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _write_chart_type(self, args):
+ # Override the virtual superclass method with a chart specific method.
+ # Write the c:scatterChart element.
+ self._write_scatter_chart(args)
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_scatter_chart(self, args):
+ # Write the element.
+
+ if args['primary_axes']:
+ series = self._get_primary_axes_series()
+ else:
+ series = self._get_secondary_axes_series()
+
+ if not len(series):
+ return
+
+ style = 'lineMarker'
+ subtype = self.subtype
+
+ # Set the user defined chart subtype.
+ if subtype == 'marker_only':
+ style = 'lineMarker'
+
+ if subtype == 'straight_with_markers':
+ style = 'lineMarker'
+
+ if subtype == 'straight':
+ style = 'lineMarker'
+
+ if subtype == 'smooth_with_markers':
+ style = 'smoothMarker'
+
+ if subtype == 'smooth':
+ style = 'smoothMarker'
+
+ # Add default formatting to the series data.
+ self._modify_series_formatting()
+
+ self._xml_start_tag('c:scatterChart')
+
+ # Write the c:scatterStyle element.
+ self._write_scatter_style(style)
+
+ # Write the series elements.
+ for data in series:
+ self._write_ser(data)
+
+ # Write the c:marker element.
+ self._write_marker_value()
+
+ # Write the c:axId elements
+ self._write_axis_ids(args)
+
+ self._xml_end_tag('c:scatterChart')
+
+ def _write_ser(self, series):
+ # Over-ridden to write c:xVal/c:yVal instead of c:cat/c:val elements.
+ # Write the element.
+
+ index = self.series_index
+ self.series_index += 1
+
+ self._xml_start_tag('c:ser')
+
+ # Write the c:idx element.
+ self._write_idx(index)
+
+ # Write the c:order element.
+ self._write_order(index)
+
+ # Write the series name.
+ self._write_series_name(series)
+
+ # Write the c:spPr element.
+ self._write_sp_pr(series)
+
+ # Write the c:marker element.
+ self._write_marker(series.get('marker'))
+
+ # Write the c:dPt element.
+ self._write_d_pt(series.get('points'))
+
+ # Write the c:dLbls element.
+ self._write_d_lbls(series.get('labels'))
+
+ # Write the c:trendline element.
+ self._write_trendline(series.get('trendline'))
+
+ # Write the c:errBars element.
+ self._write_error_bars(series.get('error_bars'))
+
+ # Write the c:xVal element.
+ self._write_x_val(series)
+
+ # Write the c:yVal element.
+ self._write_y_val(series)
+
+ # Write the c:smooth element.
+ if 'smooth' in self.subtype and series['smooth'] is None:
+ # Default is on for smooth scatter charts.
+ self._write_c_smooth(True)
+ else:
+ self._write_c_smooth(series['smooth'])
+
+ self._xml_end_tag('c:ser')
+
+ def _write_plot_area(self):
+ # Over-ridden to have 2 valAx elements for scatter charts instead
+ # of catAx/valAx.
+ #
+ # Write the element.
+ self._xml_start_tag('c:plotArea')
+
+ # Write the c:layout element.
+ self._write_layout(self.plotarea.get('layout'), 'plot')
+
+ # Write the subclass chart elements for primary and secondary axes.
+ self._write_chart_type({'primary_axes': 1})
+ self._write_chart_type({'primary_axes': 0})
+
+ # Write c:catAx and c:valAx elements for series using primary axes.
+ self._write_cat_val_axis({'x_axis': self.x_axis,
+ 'y_axis': self.y_axis,
+ 'axis_ids': self.axis_ids,
+ 'position': 'b',
+ })
+
+ tmp = self.horiz_val_axis
+ self.horiz_val_axis = 1
+
+ self._write_val_axis({'x_axis': self.x_axis,
+ 'y_axis': self.y_axis,
+ 'axis_ids': self.axis_ids,
+ 'position': 'l',
+ })
+
+ self.horiz_val_axis = tmp
+
+ # Write c:valAx and c:catAx elements for series using secondary axes
+ self._write_cat_val_axis({'x_axis': self.x2_axis,
+ 'y_axis': self.y2_axis,
+ 'axis_ids': self.axis2_ids,
+ 'position': 'b',
+ })
+ self.horiz_val_axis = 1
+ self._write_val_axis({'x_axis': self.x2_axis,
+ 'y_axis': self.y2_axis,
+ 'axis_ids': self.axis2_ids,
+ 'position': 'l',
+ })
+
+ # Write the c:spPr element for the plotarea formatting.
+ self._write_sp_pr(self.plotarea)
+
+ self._xml_end_tag('c:plotArea')
+
+ def _write_x_val(self, series):
+ # Write the element.
+ formula = series.get('categories')
+ data_id = series.get('cat_data_id')
+ data = self.formula_data[data_id]
+
+ self._xml_start_tag('c:xVal')
+
+ # Check the type of cached data.
+ data_type = self._get_data_type(data)
+
+ # TODO. Can a scatter plot have non-numeric data.
+ if data_type == 'str':
+ # Write the c:numRef element.
+ self._write_str_ref(formula, data, data_type)
+ else:
+ # Write the c:numRef element.
+ self._write_num_ref(formula, data, data_type)
+
+ self._xml_end_tag('c:xVal')
+
+ def _write_y_val(self, series):
+ # Write the element.
+ formula = series.get('values')
+ data_id = series.get('val_data_id')
+ data = self.formula_data[data_id]
+
+ self._xml_start_tag('c:yVal')
+
+ # Unlike Cat axes data should only be numeric.
+ # Write the c:numRef element.
+ self._write_num_ref(formula, data, 'num')
+
+ self._xml_end_tag('c:yVal')
+
+ def _write_scatter_style(self, val):
+ # Write the element.
+ attributes = [('val', val)]
+
+ self._xml_empty_tag('c:scatterStyle', attributes)
+
+ def _modify_series_formatting(self):
+ # Add default formatting to the series data unless it has already been
+ # specified by the user.
+ subtype = self.subtype
+
+ # The default scatter style "markers only" requires a line type.
+ if subtype == 'marker_only':
+
+ # Go through each series and define default values.
+ for series in self.series:
+
+ # Set a line type unless there is already a user defined type.
+ if not series['line']['defined']:
+ series['line'] = {'width': 2.25,
+ 'none': 1,
+ 'defined': 1,
+ }
+
+ # Turn markers off for subtypes that don't have them.
+ if 'marker' not in subtype:
+ # Go through each series and define default values.
+ for series in self.series:
+ # Set a marker type unless there is a user defined type.
+ if not series.get('marker'):
+ series['marker'] = {'type': 'none', 'defined': 1}
+
+ def _write_d_pt_point(self, index, point):
+ # Write an individual element. Override the parent method to
+ # add markers.
+
+ self._xml_start_tag('c:dPt')
+
+ # Write the c:idx element.
+ self._write_idx(index)
+
+ self._xml_start_tag('c:marker')
+
+ # Write the c:spPr element.
+ self._write_sp_pr(point)
+
+ self._xml_end_tag('c:marker')
+
+ self._xml_end_tag('c:dPt')
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_scatter.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_scatter.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_stock.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_stock.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,130 @@
+###############################################################################
+#
+# ChartStock - A class for writing the Excel XLSX Stock charts.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+from . import chart
+
+
+class ChartStock(chart.Chart):
+ """
+ A class for writing the Excel XLSX Stock charts.
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self, options=None):
+ """
+ Constructor.
+
+ """
+ super(ChartStock, self).__init__()
+
+ if options is None:
+ options = {}
+
+ self.show_crosses = 0
+ self.hi_low_lines = {}
+ self.date_category = True
+
+ # Override and reset the default axis values.
+ self.x_axis['defaults']['num_format'] = 'dd/mm/yyyy'
+ self.x2_axis['defaults']['num_format'] = 'dd/mm/yyyy'
+
+ # Set the available data label positions for this chart type.
+ self.label_position_default = 'right'
+ self.label_positions = {
+ 'center': 'ctr',
+ 'right': 'r',
+ 'left': 'l',
+ 'above': 't',
+ 'below': 'b',
+ # For backward compatibility.
+ 'top': 't',
+ 'bottom': 'b'}
+
+ self.set_x_axis({})
+ self.set_x2_axis({})
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _write_chart_type(self, args):
+ # Override the virtual superclass method with a chart specific method.
+ # Write the c:stockChart element.
+ self._write_stock_chart(args)
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_stock_chart(self, args):
+ # Write the element.
+ # Overridden to add hi_low_lines().
+
+ if args['primary_axes']:
+ series = self._get_primary_axes_series()
+ else:
+ series = self._get_secondary_axes_series()
+
+ if not len(series):
+ return
+
+ # Add default formatting to the series data.
+ self._modify_series_formatting()
+
+ self._xml_start_tag('c:stockChart')
+
+ # Write the series elements.
+ for data in series:
+ self._write_ser(data)
+
+ # Write the c:dropLines element.
+ self._write_drop_lines()
+
+ # Write the c:hiLowLines element.
+ if args.get('primary_axes'):
+ self._write_hi_low_lines()
+
+ # Write the c:upDownBars element.
+ self._write_up_down_bars()
+
+ # Write the c:marker element.
+ self._write_marker_value()
+
+ # Write the c:axId elements
+ self._write_axis_ids(args)
+
+ self._xml_end_tag('c:stockChart')
+
+ def _modify_series_formatting(self):
+ # Add default formatting to the series data.
+
+ index = 0
+
+ for series in self.series:
+ if index % 4 != 3:
+ if not series['line']['defined']:
+ series['line'] = {'width': 2.25,
+ 'none': 1,
+ 'defined': 1}
+
+ if series['marker'] is None:
+ if index % 4 == 2:
+ series['marker'] = {'type': 'dot', 'size': 3}
+ else:
+ series['marker'] = {'type': 'none'}
+
+ index += 1
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_stock.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chart_stock.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chartsheet.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chartsheet.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,179 @@
+###############################################################################
+#
+# Chartsheet - A class for writing the Excel XLSX Worksheet file.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+from . import worksheet
+from .drawing import Drawing
+
+
+class Chartsheet(worksheet.Worksheet):
+ """
+ A class for writing the Excel XLSX Chartsheet file.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self):
+ """
+ Constructor.
+
+ """
+
+ super(Chartsheet, self).__init__()
+
+ self.is_chartsheet = True
+ self.drawing = None
+ self.chart = None
+ self.charts = []
+ self.zoom_scale_normal = 0
+ self.orientation = 0
+ self.protection = False
+
+ def set_chart(self, chart):
+ """
+ Set the chart object for the chartsheet.
+ Args:
+ chart: Chart object.
+ Returns:
+ chart: A reference to the chart object.
+ """
+ chart.embedded = False
+ chart.protection = self.protection
+ self.chart = chart
+ self.charts.append([0, 0, chart, 0, 0, 1, 1])
+ return chart
+
+ def protect(self, password='', options=None):
+ """
+ Set the password and protection options of the worksheet.
+
+ Args:
+ password: An optional password string.
+ options: A dictionary of worksheet objects to protect.
+
+ Returns:
+ Nothing.
+
+ """
+ # Overridden from parent worksheet class.
+ if self.chart:
+ self.chart.protection = True
+ else:
+ self.protection = True
+
+ if not options:
+ options = {}
+
+ options = options.copy()
+
+ options['sheet'] = False
+ options['content'] = True
+ options['scenarios'] = True
+
+ # Call the parent method.
+ super(Chartsheet, self).protect(password, options)
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+ def _assemble_xml_file(self):
+ # Assemble and write the XML file.
+
+ # Write the XML declaration.
+ self._xml_declaration()
+
+ # Write the root worksheet element.
+ self._write_chartsheet()
+
+ # Write the worksheet properties.
+ self._write_sheet_pr()
+
+ # Write the sheet view properties.
+ self._write_sheet_views()
+
+ # Write the sheetProtection element.
+ self._write_sheet_protection()
+
+ # Write the printOptions element.
+ self._write_print_options()
+
+ # Write the worksheet page_margins.
+ self._write_page_margins()
+
+ # Write the worksheet page setup.
+ self._write_page_setup()
+
+ # Write the headerFooter element.
+ self._write_header_footer()
+
+ # Write the drawing element.
+ self._write_drawings()
+
+ # Close the worksheet tag.
+ self._xml_end_tag('chartsheet')
+
+ # Close the file.
+ self._xml_close()
+
+ def _prepare_chart(self, index, chart_id, drawing_id):
+ # Set up chart/drawings.
+
+ self.chart.id = chart_id - 1
+
+ self.drawing = Drawing()
+ self.drawing.orientation = self.orientation
+
+ self.external_drawing_links.append(['/drawing',
+ '../drawings/drawing'
+ + str(drawing_id)
+ + '.xml'])
+
+ self.drawing_links.append(['/chart',
+ '../charts/chart'
+ + str(chart_id)
+ + '.xml'])
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_chartsheet(self):
+ # Write the element. This is the root element.
+
+ schema = 'http://schemas.openxmlformats.org/'
+ xmlns = schema + 'spreadsheetml/2006/main'
+ xmlns_r = schema + 'officeDocument/2006/relationships'
+
+ attributes = [
+ ('xmlns', xmlns),
+ ('xmlns:r', xmlns_r)]
+
+ self._xml_start_tag('chartsheet', attributes)
+
+ def _write_sheet_pr(self):
+ # Write the element for Sheet level properties.
+ attributes = []
+
+ if self.filter_on:
+ attributes.append(('filterMode', 1))
+
+ if (self.fit_page or self.tab_color):
+ self._xml_start_tag('sheetPr', attributes)
+ self._write_tab_color()
+ self._write_page_set_up_pr()
+ self._xml_end_tag('sheetPr')
+ else:
+ self._xml_empty_tag('sheetPr', attributes)
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chartsheet.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/chartsheet.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/comments.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/comments.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,205 @@
+###############################################################################
+#
+# Comments - A class for writing the Excel XLSX Worksheet file.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+import re
+
+from . import xmlwriter
+from .utility import xl_rowcol_to_cell
+
+
+class Comments(xmlwriter.XMLwriter):
+ """
+ A class for writing the Excel XLSX Comments file.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self):
+ """
+ Constructor.
+
+ """
+
+ super(Comments, self).__init__()
+ self.author_ids = {}
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _assemble_xml_file(self, comments_data=[]):
+ # Assemble and write the XML file.
+
+ # Write the XML declaration.
+ self._xml_declaration()
+
+ # Write the comments element.
+ self._write_comments()
+
+ # Write the authors element.
+ self._write_authors(comments_data)
+
+ # Write the commentList element.
+ self._write_comment_list(comments_data)
+
+ self._xml_end_tag('comments')
+
+ # Close the file.
+ self._xml_close()
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_comments(self):
+ # Write the element.
+ xmlns = 'http://schemas.openxmlformats.org/spreadsheetml/2006/main'
+
+ attributes = [('xmlns', xmlns)]
+
+ self._xml_start_tag('comments', attributes)
+
+ def _write_authors(self, comment_data):
+ # Write the element.
+ author_count = 0
+
+ self._xml_start_tag('authors')
+
+ for comment in comment_data:
+ author = comment[3]
+
+ if author is not None and author not in self.author_ids:
+ # Store the author id.
+ self.author_ids[author] = author_count
+ author_count += 1
+
+ # Write the author element.
+ self._write_author(author)
+
+ self._xml_end_tag('authors')
+
+ def _write_author(self, data):
+ # Write the element.
+ self._xml_data_element('author', data)
+
+ def _write_comment_list(self, comment_data):
+ # Write the element.
+ self._xml_start_tag('commentList')
+
+ for comment in comment_data:
+ row = comment[0]
+ col = comment[1]
+ text = comment[2]
+ author = comment[3]
+
+ # Look up the author id.
+ author_id = None
+ if author is not None:
+ author_id = self.author_ids[author]
+
+ # Write the comment element.
+ self._write_comment(row, col, text, author_id)
+
+ self._xml_end_tag('commentList')
+
+ def _write_comment(self, row, col, text, author_id):
+ # Write the element.
+ ref = xl_rowcol_to_cell(row, col)
+
+ attributes = [('ref', ref)]
+
+ if author_id is not None:
+ attributes.append(('authorId', author_id))
+
+ self._xml_start_tag('comment', attributes)
+
+ # Write the text element.
+ self._write_text(text)
+
+ self._xml_end_tag('comment')
+
+ def _write_text(self, text):
+ # Write the element.
+ self._xml_start_tag('text')
+
+ # Write the text r element.
+ self._write_text_r(text)
+
+ self._xml_end_tag('text')
+
+ def _write_text_r(self, text):
+ # Write the element.
+ self._xml_start_tag('r')
+
+ # Write the rPr element.
+ self._write_r_pr()
+
+ # Write the text r element.
+ self._write_text_t(text)
+
+ self._xml_end_tag('r')
+
+ def _write_text_t(self, text):
+ # Write the text element.
+ attributes = []
+
+ if re.search('^\s', text) or re.search('\s$', text):
+ attributes.append(('xml:space', 'preserve'))
+
+ self._xml_data_element('t', text, attributes)
+
+ def _write_r_pr(self):
+ # Write the element.
+ self._xml_start_tag('rPr')
+
+ # Write the sz element.
+ self._write_sz()
+
+ # Write the color element.
+ self._write_color()
+
+ # Write the rFont element.
+ self._write_r_font()
+
+ # Write the family element.
+ self._write_family()
+
+ self._xml_end_tag('rPr')
+
+ def _write_sz(self):
+ # Write the element.
+ attributes = [('val', 8)]
+
+ self._xml_empty_tag('sz', attributes)
+
+ def _write_color(self):
+ # Write the element.
+ attributes = [('indexed', 81)]
+
+ self._xml_empty_tag('color', attributes)
+
+ def _write_r_font(self):
+ # Write the element.
+ attributes = [('val', 'Tahoma')]
+
+ self._xml_empty_tag('rFont', attributes)
+
+ def _write_family(self):
+ # Write the element.
+ attributes = [('val', 2)]
+
+ self._xml_empty_tag('family', attributes)
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/comments.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/comments.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/compat_collections.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/compat_collections.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,196 @@
+"""
+From the GC3Pie project: https://code.google.com/p/gc3pie/
+
+A backport of the Python standard `collections` package, providing
+`namedtuple` and `defaultdict` also on Python 2.4 and 2.5.
+
+This package actually imports your Python `collections`, and adds
+its own versions of `namedtuple` and `defaultdict` only if they are
+missing.
+"""
+
+from collections import *
+import sys
+
+try:
+ defaultdict
+except NameError:
+ class defaultdict(dict):
+ """
+ A backport of `defaultdict` to Python 2.4
+ See http://docs.python.org/library/collections.html
+ """
+ def __new__(cls, default_factory=None):
+ return dict.__new__(cls)
+
+ def __init__(self, default_factory):
+ self.default_factory = default_factory
+
+ def __missing__(self, key):
+ try:
+ return self.default_factory()
+ except:
+ raise KeyError("Key '%s' not in dictionary" % key)
+
+ def __getitem__(self, key):
+ if not dict.__contains__(self, key):
+ dict.__setitem__(self, key, self.__missing__(key))
+ return dict.__getitem__(self, key)
+
+
+try:
+ namedtuple
+except NameError:
+ # Use Raymond Hettinger's original `namedtuple` package.
+ #
+ # Source originally taken from:
+ # http://code.activestate.com/recipes/500261-named-tuples/
+ from operator import itemgetter as _itemgetter
+ from keyword import iskeyword as _iskeyword
+ import sys as _sys
+
+ def namedtuple(typename, field_names, verbose=False, rename=False):
+ """Returns a new subclass of tuple with named fields.
+
+ >>> Point = namedtuple('Point', 'x y')
+ >>> Point.__doc__ # docstring for the new class
+ 'Point(x, y)'
+ >>> p = Point(11, y=22) # instantiate with positional args or keywords
+ >>> p[0] + p[1] # indexable like a plain tuple
+ 33
+ >>> x, y = p # unpack like a regular tuple
+ >>> x, y
+ (11, 22)
+ >>> p.x + p.y # fields also accessible by name
+ 33
+ >>> d = p._asdict() # convert to a dictionary
+ >>> d['x']
+ 11
+ >>> Point(**d) # convert from a dictionary
+ Point(x=11, y=22)
+ >>> p._replace(x=100) # _replace() is like str.replace() but targets named fields
+ Point(x=100, y=22)
+
+ """
+
+ # Parse and validate the field names. Validation serves two purposes,
+ # generating informative error messages and preventing template injection attacks.
+ if isinstance(field_names, basestring):
+ field_names = field_names.replace(',', ' ').split() # names separated by whitespace and/or commas
+ field_names = tuple(map(str, field_names))
+ if rename:
+ names = list(field_names)
+ seen = set()
+ for i, name in enumerate(names):
+ if (not min(c.isalnum() or c == '_' for c in name)
+ or _iskeyword(name)
+ or not name or name[0].isdigit()
+ or name.startswith('_')
+ or name in seen):
+ names[i] = '_%d' % i
+
+ seen.add(name)
+ field_names = tuple(names)
+ for name in (typename,) + field_names:
+ if not min(c.isalnum() or c == '_' for c in name):
+ raise ValueError('Type names and field names can only contain alphanumeric characters and underscores: %r' % name)
+ if _iskeyword(name):
+ raise ValueError('Type names and field names cannot be a keyword: %r' % name)
+ if name[0].isdigit():
+ raise ValueError('Type names and field names cannot start with a number: %r' % name)
+ seen_names = set()
+ for name in field_names:
+ if name.startswith('_') and not rename:
+ raise ValueError('Field names cannot start with an underscore: %r' % name)
+ if name in seen_names:
+ raise ValueError('Encountered duplicate field name: %r' % name)
+ seen_names.add(name)
+
+ # Create and fill-in the class template
+ numfields = len(field_names)
+ argtxt = repr(field_names).replace("'", "")[1:-1] # tuple repr without parens or quotes
+ reprtxt = ', '.join('%s=%%r' % name for name in field_names)
+ template = '''class %(typename)s(tuple):
+ '%(typename)s(%(argtxt)s)' \n
+ __slots__ = () \n
+ _fields = %(field_names)r \n
+ def __new__(_cls, %(argtxt)s):
+ return _tuple.__new__(_cls, (%(argtxt)s)) \n
+ @classmethod
+ def _make(cls, iterable, new=tuple.__new__, len=len):
+ 'Make a new %(typename)s object from a sequence or iterable'
+ result = new(cls, iterable)
+ if len(result) != %(numfields)d:
+ raise TypeError('Expected %(numfields)d arguments, got %%d' %% len(result))
+ return result \n
+ def __repr__(self):
+ return '%(typename)s(%(reprtxt)s)' %% self \n
+ def _asdict(self):
+ 'Return a new dict which maps field names to their values'
+ return dict(zip(self._fields, self)) \n
+ def _replace(_self, **kwds):
+ 'Return a new %(typename)s object replacing specified fields with new values'
+ result = _self._make(map(kwds.pop, %(field_names)r, _self))
+ if kwds:
+ raise ValueError('Got unexpected field names: %%r' %% kwds.keys())
+ return result \n
+ def __getnewargs__(self):
+ return tuple(self) \n\n''' % locals()
+ for i, name in enumerate(field_names):
+ template += ' %s = _property(_itemgetter(%d))\n' % (name, i)
+ if verbose:
+ print(template)
+
+ # Execute the template string in a temporary namespace
+ namespace = dict(_itemgetter=_itemgetter, __name__='namedtuple_%s' % typename,
+ _property=property, _tuple=tuple)
+ try:
+ exec(template) in namespace
+ except SyntaxError:
+ e = sys.exc_info()[1]
+ raise SyntaxError(str(e) + ':\n' + template)
+ result = namespace[typename]
+
+ # For pickling to work, the __module__ variable needs to be set to the frame
+ # where the named tuple is created. Bypass this step in environments where
+ # sys._getframe is not defined (Jython for example) or sys._getframe is not
+ # defined for arguments greater than 0 (IronPython).
+ try:
+ result.__module__ = _sys._getframe(1).f_globals.get('__name__', '__main__')
+ except (AttributeError, ValueError):
+ pass
+
+ return result
+
+
+if __name__ == '__main__':
+ # verify that instances can be pickled
+ from cPickle import loads, dumps
+ Point = namedtuple('Point', 'x, y', True)
+ p = Point(x=10, y=20)
+ assert p == loads(dumps(p, -1))
+
+ # test and demonstrate ability to override methods
+ class Point(namedtuple('Point', 'x y')):
+ @property
+ def hypot(self):
+ return (self.x ** 2 + self.y ** 2) ** 0.5
+
+ def __str__(self):
+ return 'Point: x=%6.3f y=%6.3f hypot=%6.3f' % (self.x, self.y, self.hypot)
+
+ for p in Point(3, 4), Point(14, 5), Point(9. / 7, 6):
+ print(p)
+
+ class Point(namedtuple('Point', 'x y')):
+ 'Point class with optimized _make() and _replace() without error-checking'
+ _make = classmethod(tuple.__new__)
+
+ def _replace(self, _map=map, **kwds):
+ return self._make(_map(kwds.get, ('x', 'y'), self))
+
+ print(Point(11, 22)._replace(x=100))
+
+ import doctest
+ TestResults = namedtuple('TestResults', 'failed attempted')
+ print(TestResults(*doctest.testmod()))
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/compat_collections.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/compat_collections.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/compatibility.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/compatibility.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,52 @@
+###############################################################################
+#
+# Python 2/3 compatibility functions for XlsxWriter.
+#
+# Copyright (c), 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+import sys
+from decimal import Decimal
+
+try:
+ # For compatibility between Python 2 and 3.
+ from StringIO import StringIO
+except ImportError:
+ from io import StringIO
+
+try:
+ # For Python 2.6+.
+ from fractions import Fraction
+except ImportError:
+ Fraction = float
+
+try:
+ # For Python 2.6+.
+ from collections import defaultdict
+ from collections import namedtuple
+except ImportError:
+ # For Python 2.5 support.
+ from .compat_collections import defaultdict
+ from .compat_collections import namedtuple
+
+# Types to check in Python 2/3.
+if sys.version_info[0] == 2:
+ num_types = (float, int, long, Decimal, Fraction)
+ str_types = basestring
+else:
+ num_types = (float, int, Decimal, Fraction)
+ str_types = str
+
+
+if sys.version_info < (2, 6, 0):
+ from StringIO import StringIO as BytesIO
+else:
+ from io import BytesIO as BytesIO
+
+
+def force_unicode(string):
+ """Return string as a native string"""
+ if sys.version_info[0] == 2:
+ if isinstance(string, unicode):
+ return string.encode('utf-8')
+ return string
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/compatibility.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/compatibility.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/contenttypes.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/contenttypes.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,197 @@
+###############################################################################
+#
+# ContentTypes - A class for writing the Excel XLSX ContentTypes file.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+import copy
+from . import xmlwriter
+
+# Long namespace strings used in the class.
+app_package = 'application/vnd.openxmlformats-package.'
+app_document = 'application/vnd.openxmlformats-officedocument.'
+
+defaults = [
+ ['rels', app_package + 'relationships+xml'],
+ ['xml', 'application/xml'],
+]
+
+overrides = [
+ ['/docProps/app.xml', app_document + 'extended-properties+xml'],
+ ['/docProps/core.xml', app_package + 'core-properties+xml'],
+ ['/xl/styles.xml', app_document + 'spreadsheetml.styles+xml'],
+ ['/xl/theme/theme1.xml', app_document + 'theme+xml'],
+ ['/xl/workbook.xml', app_document + 'spreadsheetml.sheet.main+xml'],
+]
+
+
+class ContentTypes(xmlwriter.XMLwriter):
+ """
+ A class for writing the Excel XLSX ContentTypes file.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self):
+ """
+ Constructor.
+
+ """
+
+ super(ContentTypes, self).__init__()
+
+ # Copy the defaults in case we need to change them.
+ self.defaults = copy.deepcopy(defaults)
+ self.overrides = copy.deepcopy(overrides)
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _assemble_xml_file(self):
+ # Assemble and write the XML file.
+
+ # Write the XML declaration.
+ self._xml_declaration()
+
+ self._write_types()
+ self._write_defaults()
+ self._write_overrides()
+
+ self._xml_end_tag('Types')
+
+ # Close the file.
+ self._xml_close()
+
+ def _add_default(self, default):
+ # Add elements to the ContentTypes defaults.
+ self.defaults.append(default)
+
+ def _add_override(self, override):
+ # Add elements to the ContentTypes overrides.
+ self.overrides.append(override)
+
+ def _add_worksheet_name(self, worksheet_name):
+ # Add the name of a worksheet to the ContentTypes overrides.
+ worksheet_name = "/xl/worksheets/" + worksheet_name + ".xml"
+
+ self._add_override((worksheet_name,
+ app_document + 'spreadsheetml.worksheet+xml'))
+
+ def _add_chartsheet_name(self, chartsheet_name):
+ # Add the name of a chartsheet to the ContentTypes overrides.
+ chartsheet_name = "/xl/chartsheets/" + chartsheet_name + ".xml"
+
+ self._add_override((chartsheet_name,
+ app_document + 'spreadsheetml.chartsheet+xml'))
+
+ def _add_chart_name(self, chart_name):
+ # Add the name of a chart to the ContentTypes overrides.
+ chart_name = "/xl/charts/" + chart_name + ".xml"
+
+ self._add_override((chart_name, app_document + 'drawingml.chart+xml'))
+
+ def _add_drawing_name(self, drawing_name):
+ # Add the name of a drawing to the ContentTypes overrides.
+ drawing_name = "/xl/drawings/" + drawing_name + ".xml"
+
+ self._add_override((drawing_name, app_document + 'drawing+xml'))
+
+ def _add_vml_name(self):
+ # Add the name of a VML drawing to the ContentTypes defaults.
+ self._add_default(('vml', app_document + 'vmlDrawing'))
+
+ def _add_comment_name(self, comment_name):
+ # Add the name of a comment to the ContentTypes overrides.
+ comment_name = "/xl/" + comment_name + ".xml"
+
+ self._add_override((comment_name,
+ app_document + 'spreadsheetml.comments+xml'))
+
+ def _add_shared_strings(self):
+ # Add the sharedStrings link to the ContentTypes overrides.
+ self._add_override(('/xl/sharedStrings.xml',
+ app_document + 'spreadsheetml.sharedStrings+xml'))
+
+ def _add_calc_chain(self):
+ # Add the calcChain link to the ContentTypes overrides.
+ self._add_override(('/xl/calcChain.xml',
+ app_document + 'spreadsheetml.calcChain+xml'))
+
+ def _add_image_types(self, image_types):
+ # Add the image default types.
+ for image_type in image_types:
+ self._add_default((image_type, 'image/' + image_type))
+
+ def _add_table_name(self, table_name):
+ # Add the name of a table to the ContentTypes overrides.
+ table_name = "/xl/tables/" + table_name + ".xml"
+
+ self._add_override((table_name,
+ app_document + 'spreadsheetml.table+xml'))
+
+ def _add_vba_project(self):
+ # Add a vbaProject to the ContentTypes defaults.
+
+ # Change the workbook.xml content-type from xlsx to xlsm.
+ for i, override in enumerate(self.overrides):
+ if override[0] == '/xl/workbook.xml':
+ self.overrides[i][1] = 'application/vnd.ms-excel.' \
+ 'sheet.macroEnabled.main+xml'
+
+ self._add_default(('bin', 'application/vnd.ms-office.vbaProject'))
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_defaults(self):
+ # Write out all of the types.
+
+ for extension, content_type in self.defaults:
+ self._xml_empty_tag('Default',
+ [('Extension', extension),
+ ('ContentType', content_type)])
+
+ def _write_overrides(self):
+ # Write out all of the types.
+ for part_name, content_type in self.overrides:
+ self._xml_empty_tag('Override',
+ [('PartName', part_name),
+ ('ContentType', content_type)])
+
+ def _write_types(self):
+ # Write the element.
+ xmlns = 'http://schemas.openxmlformats.org/package/2006/content-types'
+
+ attributes = [('xmlns', xmlns,)]
+ self._xml_start_tag('Types', attributes)
+
+ def _write_default(self, extension, content_type):
+ # Write the element.
+ attributes = [
+ ('Extension', extension),
+ ('ContentType', content_type),
+ ]
+
+ self._xml_empty_tag('Default', attributes)
+
+ def _write_override(self, part_name, content_type):
+ # Write the element.
+ attributes = [
+ ('PartName', part_name),
+ ('ContentType', content_type),
+ ]
+
+ self._xml_empty_tag('Override', attributes)
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/contenttypes.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/contenttypes.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/core.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/core.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,192 @@
+###############################################################################
+#
+# Core - A class for writing the Excel XLSX Worksheet file.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+# Standard packages.
+from datetime import datetime
+
+# Package imports.
+from . import xmlwriter
+
+
+class Core(xmlwriter.XMLwriter):
+ """
+ A class for writing the Excel XLSX Core file.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self):
+ """
+ Constructor.
+
+ """
+
+ super(Core, self).__init__()
+
+ self.properties = {}
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _assemble_xml_file(self):
+ # Assemble and write the XML file.
+
+ # Write the XML declaration.
+ self._xml_declaration()
+
+ self._write_cp_core_properties()
+ self._write_dc_title()
+ self._write_dc_subject()
+ self._write_dc_creator()
+ self._write_cp_keywords()
+ self._write_dc_description()
+ self._write_cp_last_modified_by()
+ self._write_dcterms_created()
+ self._write_dcterms_modified()
+ self._write_cp_category()
+ self._write_cp_content_status()
+
+ self._xml_end_tag('cp:coreProperties')
+
+ # Close the file.
+ self._xml_close()
+
+ def _set_properties(self, properties):
+ # Set the document properties.
+ self.properties = properties
+
+ def _localtime_to_iso8601_date(self, date):
+ # Convert to a ISO 8601 style "2010-01-01T00:00:00Z" date.
+ if not date:
+ date = datetime.now()
+
+ return date.strftime("%Y-%m-%dT%H:%M:%SZ")
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_cp_core_properties(self):
+ # Write the element.
+
+ xmlns_cp = ('http://schemas.openxmlformats.org/package/2006/' +
+ 'metadata/core-properties')
+ xmlns_dc = 'http://purl.org/dc/elements/1.1/'
+ xmlns_dcterms = 'http://purl.org/dc/terms/'
+ xmlns_dcmitype = 'http://purl.org/dc/dcmitype/'
+ xmlns_xsi = 'http://www.w3.org/2001/XMLSchema-instance'
+
+ attributes = [
+ ('xmlns:cp', xmlns_cp),
+ ('xmlns:dc', xmlns_dc),
+ ('xmlns:dcterms', xmlns_dcterms),
+ ('xmlns:dcmitype', xmlns_dcmitype),
+ ('xmlns:xsi', xmlns_xsi),
+ ]
+
+ self._xml_start_tag('cp:coreProperties', attributes)
+
+ def _write_dc_creator(self):
+ # Write the element.
+ data = self.properties.get('author', '')
+
+ self._xml_data_element('dc:creator', data)
+
+ def _write_cp_last_modified_by(self):
+ # Write the element.
+ data = self.properties.get('author', '')
+
+ self._xml_data_element('cp:lastModifiedBy', data)
+
+ def _write_dcterms_created(self):
+ # Write the element.
+ date = self.properties.get('created', datetime.now())
+
+ xsi_type = 'dcterms:W3CDTF'
+
+ date = self._localtime_to_iso8601_date(date)
+
+ attributes = [('xsi:type', xsi_type,)]
+
+ self._xml_data_element('dcterms:created', date, attributes)
+
+ def _write_dcterms_modified(self):
+ # Write the element.
+ date = self.properties.get('created', datetime.now())
+
+ xsi_type = 'dcterms:W3CDTF'
+
+ date = self._localtime_to_iso8601_date(date)
+
+ attributes = [('xsi:type', xsi_type,)]
+
+ self._xml_data_element('dcterms:modified', date, attributes)
+
+ def _write_dc_title(self):
+ # Write the element.
+ if 'title' in self.properties:
+ data = self.properties['title']
+ else:
+ return
+
+ self._xml_data_element('dc:title', data)
+
+ def _write_dc_subject(self):
+ # Write the element.
+ if 'subject' in self.properties:
+ data = self.properties['subject']
+ else:
+ return
+
+ self._xml_data_element('dc:subject', data)
+
+ def _write_cp_keywords(self):
+ # Write the element.
+ if 'keywords' in self.properties:
+ data = self.properties['keywords']
+ else:
+ return
+
+ self._xml_data_element('cp:keywords', data)
+
+ def _write_dc_description(self):
+ # Write the element.
+ if 'comments' in self.properties:
+ data = self.properties['comments']
+ else:
+ return
+
+ self._xml_data_element('dc:description', data)
+
+ def _write_cp_category(self):
+ # Write the element.
+ if 'category' in self.properties:
+ data = self.properties['category']
+ else:
+ return
+
+ self._xml_data_element('cp:category', data)
+
+ def _write_cp_content_status(self):
+ # Write the element.
+ if 'status' in self.properties:
+ data = self.properties['status']
+ else:
+ return
+
+ self._xml_data_element('cp:contentStatus', data)
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/core.pyc
Binary file test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/core.pyc has changed
diff -r 000000000000 -r 0abe6bac47a6 test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/drawing.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test.tool_dependencies.rnachipintegrator/rnachipintegrator/1.0.0/lib/python2.7/site-packages/xlsxwriter/drawing.py Wed Feb 24 09:25:18 2016 -0500
@@ -0,0 +1,1096 @@
+###############################################################################
+#
+# Drawing - A class for writing the Excel XLSX Drawing file.
+#
+# Copyright 2013-2016, John McNamara, jmcnamara@cpan.org
+#
+
+import re
+
+from . import xmlwriter
+from .shape import Shape
+from .utility import get_rgb_color
+
+
+class Drawing(xmlwriter.XMLwriter):
+ """
+ A class for writing the Excel XLSX Drawing file.
+
+
+ """
+
+ ###########################################################################
+ #
+ # Public API.
+ #
+ ###########################################################################
+
+ def __init__(self):
+ """
+ Constructor.
+
+ """
+
+ super(Drawing, self).__init__()
+
+ self.drawings = []
+ self.embedded = 0
+ self.orientation = 0
+
+ ###########################################################################
+ #
+ # Private API.
+ #
+ ###########################################################################
+
+ def _assemble_xml_file(self):
+ # Assemble and write the XML file.
+
+ # Write the XML declaration.
+ self._xml_declaration()
+
+ # Write the xdr:wsDr element.
+ self._write_drawing_workspace()
+
+ if self.embedded:
+ index = 1
+ for drawing in self.drawings:
+ # Write the xdr:twoCellAnchor element.
+ self._write_two_cell_anchor(index, drawing)
+ index += 1
+
+ if drawing['url']:
+ index += 1
+
+ else:
+ # Write the xdr:absoluteAnchor element.
+ self._write_absolute_anchor(1)
+
+ self._xml_end_tag('xdr:wsDr')
+
+ # Close the file.
+ self._xml_close()
+
+ def _add_drawing_object(self, drawing_object):
+ # Add a chart, image or shape sub object to the drawing.
+
+ obj = {
+ 'anchor_type': drawing_object[0],
+ 'col_from': drawing_object[1],
+ 'row_from': drawing_object[2],
+ 'col_from_offset': drawing_object[3],
+ 'row_from_offset': drawing_object[4],
+ 'col_to': drawing_object[5],
+ 'row_to': drawing_object[6],
+ 'col_to_offset': drawing_object[7],
+ 'row_to_offset': drawing_object[8],
+ 'col_absolute': drawing_object[9],
+ 'row_absolute': drawing_object[10],
+ 'width': drawing_object[11],
+ 'height': drawing_object[12],
+ 'description': drawing_object[13],
+ 'shape': drawing_object[14],
+ 'url': None,
+ 'tip': None,
+ 'anchor': None
+ }
+
+ if len(drawing_object) > 15:
+ obj['url'] = drawing_object[15]
+ obj['tip'] = drawing_object[16]
+ obj['anchor'] = drawing_object[17]
+
+ self.drawings.append(obj)
+
+ ###########################################################################
+ #
+ # XML methods.
+ #
+ ###########################################################################
+
+ def _write_drawing_workspace(self):
+ # Write the