lastz_paired_reads: lastz_paired_reads

annotate lastz_paired_reads_wrapper.py @ 0:643f8a898a36 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b

author	devteam
date	Mon, 09 Nov 2015 11:41:55 -0500
parents
children

rev	line source
0 643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	1 #!/usr/bin/env python
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	2
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	3 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	4 Runs Lastz paired read alignment process
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	5 Written for Lastz v. 1.02.00.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	6
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	7 # Author(s): based on various scripts written by Bob Harris (rsharris@bx.psu.edu),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	8 # then tweaked to this form by Greg Von Kuster (greg@bx.psu.edu)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	9
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	10 This tool takes the following input:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	11 a. A collection of 454 paired end reads ( a fasta file )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	12 b. A linker sequence ( a very small fasta file )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	13 c. A reference genome ( nob, 2bit or fasta )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	14
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	15 and uses the following process:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	16 1. Split reads into mates: the input to this step is the read file XXX.fasta, and the output is three
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	17 files; XXX.short.fasta, XXX.long.fasta and XXX.mapping. The mapping file records the information necessary
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	18 to convert mate coordinates back into the original read, which is needed later in the process.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	19
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	20 2. Align short mates to the reference: this runs lastz against every chromosome. The input is XXX.short.fasta
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	21 and the reference genome, and the output is a SAM file, XXX.short.sam.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	22
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	23 3. Align long mates to the reference: this runs lastz against every chromosome. The input is XXX.long.fasta
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	24 and the reference genome, and the output is a SAM file, XXX.long.sam.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	25
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	26 4. Combine, and convert mate coordinates back to read coordinates. The input is XXX.mapping, XXX.short.sam and
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	27 XXX.long.sam, and the output is XXX.sam.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	28
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	29 usage: lastz_paired_reads_wrapper.py [options]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	30 --ref_name: The reference name to change all output matches to
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	31 --ref_source: The reference is cached or from the history
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	32 --source_select: Use pre-set or cached reference file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	33 --input1: The name of the reference file if using history or reference base name if using cached
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	34 --input2: The reads file to align
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	35 --input3: The sequencing linker file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	36 --input4: The base quality score 454 file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	37 --ref_sequences: The number of sequences in the reference file if using one from history
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	38 --output: The name of the output file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	39 --lastz_seqs_file_dir: Directory of local lastz_seqs.loc file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	40 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	41 import optparse, os, subprocess, shutil, sys, tempfile, time
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	42 from string import maketrans
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	43
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	44 from galaxy import eggs
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	45 import pkg_resources
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	46 pkg_resources.require( 'bx-python' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	47 from bx.seq.twobit import *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	48 from bx.seq.fasta import FastaReader
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	49 from galaxy.util.bunch import Bunch
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	50 from galaxy.util import string_as_bool
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	51
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	52 # Column indexes for SAM required fields
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	53 SAM_QNAME_COLUMN = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	54 SAM_FLAG_COLUMN = 1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	55 SAM_RNAME_COLUMN = 2
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	56 SAM_POS_COLUMN = 3
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	57 SAM_MAPQ_COLUMN = 4
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	58 SAM_CIGAR_COLUMN = 5
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	59 SAM_MRNM_COLUMN = 6
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	60 SAM_MPOS_COLUMN = 7
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	61 SAM_ISIZE_COLUMN = 8
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	62 SAM_SEQ_COLUMN = 9
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	63 SAM_QUAL_COLUMN = 10
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	64 SAM_MIN_COLUMNS = 11
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	65 # SAM bit-encoded flags
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	66 BAM_FPAIRED = 1 # the read is paired in sequencing, no matter whether it is mapped in a pair
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	67 BAM_FPROPER_PAIR = 2 # the read is mapped in a proper pair
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	68 BAM_FUNMAP = 4 # the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	69 BAM_FMUNMAP = 8 # the mate is unmapped
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	70 BAM_FREVERSE = 16 # the read is mapped to the reverse strand
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	71 BAM_FMREVERSE = 32 # the mate is mapped to the reverse strand
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	72 BAM_FREAD1 = 64 # this is read1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	73 BAM_FREAD2 = 128 # this is read2
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	74 BAM_FSECONDARY = 256 # not primary alignment
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	75 BAM_FQCFAIL = 512 # QC failure
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	76 BAM_FDUP = 1024 # optical or PCR duplicate
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	77
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	78 # Keep track of all created temporary files so they can be deleted
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	79 global tmp_file_names
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	80 tmp_file_names = []
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	81 # The values in the skipped_lines dict are tuples consisting of:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	82 # - the number of skipped lines for that error
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	83 # If not a sequence error:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	84 # - the 1st line number on which the error was found
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	85 # - the text of the 1st line on which the error was found
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	86 # If a sequence error:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	87 # - The number of the sequence in the file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	88 # - the sequence name on which the error occurred
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	89 # We may need to improve dealing with file position and text as
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	90 # much of it comes from temporary files that are created from the
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	91 # inputs, and not the inputs themselves, so this could be confusing
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	92 # to the user.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	93 global skipped_lines
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	94 skipped_lines = dict( bad_interval=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	95 inconsistent_read_lengths=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	96 inconsistent_reads=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	97 inconsistent_sizes=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	98 missing_mate=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	99 missing_quals=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	100 missing_seq=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	101 multiple_seqs=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	102 no_header=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	103 num_fields=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	104 reads_paired=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	105 sam_flag=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	106 sam_headers=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	107 sam_min_columns=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	108 two_mate_names=( 0, 0, '' ),
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	109 wrong_seq_len=( 0, 0, '' ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	110 global total_skipped_lines
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	111 total_skipped_lines = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	112
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	113 def stop_err( msg ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	114 sys.stderr.write( "%s" % msg )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	115 sys.exit()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	116
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	117 def skip_line( error_key, position, text ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	118 if not skipped_lines[ error_key ][2]:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	119 skipped_lines[ error_key ][1] = position
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	120 skipped_lines[ error_key ][2] = text
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	121 skipped_lines[ error_key ][0] += 1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	122 total_skipped_lines += 1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	123
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	124 def get_tmp_file_name( dir=None, suffix=None ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	125 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	126 Return a unique temporary file name that can be managed. The
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	127 file must be manually removed after use.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	128 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	129 if dir and suffix:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	130 tmp_fd, tmp_name = tempfile.mkstemp( dir=dir, suffix=suffix )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	131 elif dir:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	132 tmp_fd, tmp_name = tempfile.mkstemp( dir=dir )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	133 elif suffix:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	134 tmp_fd, tmp_name = tempfile.mkstemp( suffix=suffix )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	135 os.close( tmp_fd )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	136 tmp_file_names.append( tmp_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	137 return tmp_name
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	138
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	139 def run_command( command ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	140 proc = subprocess.Popen( args=command, shell=True, stderr=subprocess.PIPE, )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	141 proc.wait()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	142 stderr = proc.stderr.read()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	143 proc.wait()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	144 if stderr:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	145 stop_err( stderr )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	146
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	147 def split_paired_reads( input2, combined_linker_file_name ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	148 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	149 Given a fasta file of allegedly paired end reads ( input2 ), and a list of intervals
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	150 showing where the linker is on each read ( combined_linker_file_name ), split the reads into left and right
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	151 halves.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	152
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	153 The input intervals look like this. Note that they may include multiple intervals for the same read
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	154 ( which should overlap ), and we use the union of them as the linker interval. Non-overlaps are
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	155 reported to the user, and those reads are not processed. Starts are origin zero.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	156
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	157 #name strand start len size
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	158 FG3OYDA05FTEES + 219 42 283
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	159 FG3OYDA05FVOLL + 263 41 416
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	160 FG3OYDA05FFL7J + 81 42 421
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	161 FG3OYDA05FOQWE + 55 42 332
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	162 FG3OYDA05FV4DW + 297 42 388
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	163 FG3OYDA05FWAQV + 325 42 419
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	164 FG3OYDA05FVLGA + 90 42 367
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	165 FG3OYDA05FWJ71 + 58 42 276
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	166
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	167 The output gives each half-sequence on a separate line, like this. This allows easy sorting of the
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	168 sequences by length, after the fact.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	169
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	170 219 FG3OYDA05FTEES_L TTTAGTTACACTTAACTCACTTCCATCCTCTAAATACGTGATTACCTTTC...
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	171 22 FG3OYDA05FTEES_R CCTTCCTTAAGTCCTAAAACTG
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	172 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	173 # Bob says these should be hard-coded.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	174 seq_len_lower_threshold = 17
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	175 short_mate_cutoff = 50
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	176 # We need to pass the name of this file back to the caller.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	177 tmp_mates_file_name = get_tmp_file_name( suffix='mates.txt' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	178 mates_file = file( tmp_mates_file_name, "w+b" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	179 # Read the linker intervals
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	180 combined_linker_file = file( combined_linker_file_name, "rb" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	181 read_to_linker_dict = {}
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	182 i = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	183 for i, line in enumerate( combined_linker_file ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	184 line = line.strip()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	185 if line.startswith( "#" ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	186 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	187 if line.find( '#' ) >= 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	188 line = line.split( "#", 1 )[0].rstrip()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	189 fields = line.split()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	190 if len( fields ) != 4:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	191 skip_line( 'num_fields', i+1, line )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	192 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	193 name, start, length, size = fields
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	194 start = int( start )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	195 length = int( length )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	196 size = int( size )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	197 end = start + length
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	198 if end > size:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	199 skip_line[ 'bad_interval' ] += 1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	200 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	201 if name not in read_to_linker_dict:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	202 read_to_linker_dict[ name ] = ( start, end, size )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	203 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	204 if read_to_linker_dict[ name ] == None:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	205 # Read previously marked as non-overlapping intervals, so skip this sequence - see below
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	206 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	207 ( s, e, sz ) = read_to_linker_dict[ name ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	208 if sz != size:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	209 skip_line( 'inconsistent_sizes', i+1, name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	210 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	211 if s > end or e < start:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	212 # Non-overlapping intervals, so skip this sequence
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	213 read_to_linker_dict[ name ] = None
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	214 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	215 read_to_linker_dict[ name ] = ( min( s, start ), max( e, end ), size )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	216 combined_linker_file.close()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	217 # We need to pass the name of this file back to the caller.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	218 tmp_mates_mapping_file_name = get_tmp_file_name( suffix='mates.mapping' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	219 mates_mapping_file = file( tmp_mates_mapping_file_name, 'w+b' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	220 # Process the sequences
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	221 seqs = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	222 fasta_reader = FastaReader( file( input2, 'rb' ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	223 while True:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	224 seq = fasta_reader.next()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	225 if not seq:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	226 break
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	227 seqs += 1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	228 if seq.name not in read_to_linker_dict:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	229 if seq.length > seq_len_lower_threshold:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	230 mates_file.write( "%-3d %s %s\n" % ( seq.length, seq.name, seq.text ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	231 read_to_linker_dict[ seq.name ] = ""
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	232 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	233 if read_to_linker_dict[ seq.name ] == "":
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	234 skip_line( 'multiple_seqs', seqs, seq.name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	235 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	236 if read_to_linker_dict[ seq.name ] == None:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	237 # Read previously marked as non-overlapping intervals, so skip this sequence - see above
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	238 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	239 ( start, end, size ) = read_to_linker_dict[ seq.name ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	240 if seq.length != size:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	241 skip_line( 'wrong_seq_len', seqs, seq.name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	242 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	243 left = seq.text[ :start ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	244 right = seq.text[ end: ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	245 left_is_small = len( left ) <= seq_len_lower_threshold
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	246 right_is_small = len( right ) <= seq_len_lower_threshold
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	247 if left_is_small and right_is_small:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	248 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	249 if not left_is_small:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	250 mates_file.write( "%-3d %s %s\n" % ( len( left ), seq.name + "_L", left ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	251 mates_mapping_file.write( "%s %s %s %s\n" % ( seq.name + "_L", seq.name, 0, size - start ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	252 if not right_is_small:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	253 mates_file.write( "%-3d %s %s\n" % ( len( right ), seq.name + "_R", right ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	254 mates_mapping_file.write( "%s %s %s %s\n" % ( seq.name + "_R", seq.name, end, 0 ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	255 read_to_linker_dict[ seq.name ] = ""
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	256 combined_linker_file.close()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	257 mates_file.close()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	258 mates_mapping_file.close()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	259 # Create temporary files for short and long mates
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	260 tmp_mates_short_file_name = get_tmp_file_name( suffix='mates.short' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	261 tmp_mates_long_file_name = get_tmp_file_name( suffix='mates.long' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	262 tmp_mates_short = open( tmp_mates_short_file_name, 'w+b' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	263 tmp_mates_long = open( tmp_mates_long_file_name, 'w+b' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	264 i = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	265 for i, line in enumerate( file( tmp_mates_file_name, 'rb' ) ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	266 fields = line.split()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	267 seq_len = int( fields[0] )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	268 seq_name = fields[1]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	269 seq_text = fields[2]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	270 if seq_len <= short_mate_cutoff:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	271 tmp_mates_short.write( ">%s\n%s\n" % ( seq_name, seq_text ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	272 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	273 tmp_mates_long.write( ">%s\n%s\n" % ( seq_name, seq_text ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	274 tmp_mates_short.close()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	275 tmp_mates_long.close()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	276 return tmp_mates_mapping_file_name, tmp_mates_file_name, tmp_mates_short_file_name, tmp_mates_long_file_name
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	277
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	278 def align_mates( input1, ref_source, ref_name, ref_sequences, tmp_mates_short_file_name, tmp_mates_long_file_name ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	279 tmp_align_file_names = []
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	280 if ref_source == 'history':
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	281 # Reference is a fasta dataset from the history
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	282 # Create temporary files to contain the output from lastz executions
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	283 tmp_short_file_name = get_tmp_file_name( suffix='short_out' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	284 tmp_align_file_names.append( tmp_short_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	285 tmp_long_file_name = get_tmp_file_name( suffix='long_out' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	286 tmp_align_file_names.append( tmp_long_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	287 seqs = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	288 fasta_reader = FastaReader( open( input1 ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	289 while True:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	290 # Read the next sequence from the reference dataset. Note that if the reference contains
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	291 # a small number of chromosomes this loop is ok, but in many cases the genome has a bunch
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	292 # of small straggler scaffolds and contigs and it is a computational waste to do each one
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	293 # of these in its own run. There is an I/O down side to running by subsets (even if they are
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	294 # one sequence per subset), compared to splitting the reference into sizes of 250 mb. With
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	295 # the subset action, lastz still has to read and parse the entire file for every run (this
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	296 # is true for fasta, but for .2bit files it can access each sequence directly within the file,
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	297 # so the overhead is minimal).
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	298 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	299 :> output_file (this creates the output file, empty)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	300 while there are more sequences to align
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	301 find the next sequences that add up to 250M, put their names in farf.names
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	302 lastz ${refFile}[subset=farf.names][multi][unmask] ${matesPath}/${matesFile} ...
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	303 >> output_file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	304 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	305 seq = fasta_reader.next()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	306 if not seq:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	307 break
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	308 seqs += 1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	309 # Create a temporary file to contain the current sequence as input to lastz.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	310 # We're doing this a bit differently here since we could be generating a huge
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	311 # number of temporary files.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	312 tmp_in_fd, tmp_in_file_name = tempfile.mkstemp( suffix='seq_%d_in' % seqs )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	313 tmp_in_file = os.fdopen( tmp_in_fd, 'w+b' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	314 tmp_in_file.write( '>%s\n%s\n' % ( seq.name, seq.text ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	315 tmp_in_file.close()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	316 # Align short mates
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	317 command = 'lastz %s[unmask]%s %s ' % ( tmp_in_file_name, ref_name, tmp_mates_short_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	318 command += 'Z=1 --seed=1111111011111 --notrans --maxwordcount=90% --match=1,3 O=1 E=3 X=15 K=10 Y=12 L=18 --ambiguousn --noytrim --identity=95 --coverage=80 --continuity=95 --format=softsam- '
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	319 command += '>> %s' % tmp_short_file_name
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	320 run_command( command )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	321 # Align long mates
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	322 command = 'lastz %s[unmask]%s %s ' % ( tmp_in_file_name, ref_name, tmp_mates_long_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	323 command += 'Z=15 W=13 --notrans --exact=18 --maxwordcount=90% --match=1,3 O=1 E=3 Y=10 L=18 --ambiguousn --noytrim --identity=95 --coverage=90 --continuity=95 --format=softsam- '
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	324 command += '>> %s' % tmp_long_file_name
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	325 run_command( command )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	326 # Remove the temporary file that contains the current sequence
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	327 os.remove( tmp_in_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	328 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	329 # Reference is a locally cached 2bit file, split lastz calls across number of chroms in 2bit file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	330 tbf = TwoBitFile( open( input1, 'rb' ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	331 for chrom in tbf.keys():
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	332 # Align short mates
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	333 tmp_short_file_name = get_tmp_file_name( suffix='short_vs_%s' % chrom )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	334 tmp_align_file_names.append( tmp_short_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	335 command = 'lastz %s/%s[unmask]%s %s ' % ( input1, chrom, ref_name, tmp_mates_short_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	336 command += 'Z=1 --seed=1111111011111 --notrans --maxwordcount=90% --match=1,3 O=1 E=3 X=15 K=10 Y=12 L=18 --ambiguousn --noytrim --identity=95 --coverage=80 --continuity=95 --format=softsam- '
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	337 command += '> %s' % tmp_short_file_name
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	338 run_command( command )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	339 # Align long mates
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	340 tmp_long_file_name = get_tmp_file_name( suffix='long_vs_%s' % chrom )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	341 tmp_align_file_names.append( tmp_long_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	342 command = 'lastz %s/%s[unmask]%s %s ' % ( input1, chrom, ref_name, tmp_mates_long_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	343 command += 'Z=15 W=13 --notrans --exact=18 --maxwordcount=90% --match=1,3 O=1 E=3 Y=10 L=18 --ambiguousn --noytrim --identity=95 --coverage=90 --continuity=95 --format=softsam- '
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	344 command += '> %s' % tmp_long_file_name
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	345 run_command( command )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	346 return tmp_align_file_names
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	347
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	348 def paired_mate_unmapper( input2, input4, tmp_mates_mapping_file_name, tmp_align_file_name_list, output ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	349 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	350 Given a SAM file corresponding to alignments of subsegments of paired 'reads' to a reference sequence,
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	351 convert the positions on the subsegments to positions on the reads. Also (optionally) add quality values.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	352
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	353 The input file is in SAM format, as shown below. Each line represents the alignment of a part of a read
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	354 to a reference sequence. Read pairs are indicated by suffixes in their names. Normally, the suffixes _L
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	355 and _R indicate the left and right mates of reads (this can be overridden with the --left and --right
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	356 options). Reads that were not mates have no suffix.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	357
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	358 (SAM header lines omitted)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	359 F2YP0BU02G7LK5_R 16 chr21 15557360 255 40M * 0 0 ATTTTATTCTCTTTGAAGCAATTGTGAATGGGAGTTTACT *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	360 F2YP0BU02HXV58_L 16 chr21 15952091 255 40M6S * 0 0 GCAAATTGTGCTGCTTTAAACATGCGTGTGCAAGTATCTTtttcat *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	361 F2YP0BU02HREML_R 0 chr21 16386077 255 33M5S * 0 0 CCAAAGTTCTGGGATTACAGGCGTGAGCCATCGcgccc *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	362 F2YP0BU02IOF1F_L 0 chr21 17567321 255 7S28M * 0 0 taaagagAAGAATTCTCAACCCAGAATTTCATATC *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	363 F2YP0BU02IKX84_R 16 chr21 18491628 255 22M1D18M9S * 0 0 GTCTCTACCAAAAAATACAAAAATTAGCCGGGCGTGGTGGcatgtctgt *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	364 F2YP0BU02GW5VA_L 16 chr21 20255344 255 6S32M * 0 0 caagaaCAAACACATTCAAAAGCTAGTAGAAGGCAAGA *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	365 F2YP0BU02JIMJ4_R 0 chr21 22383051 255 19M * 0 0 CCCTTTATCATTTTTTATT *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	366 F2YP0BU02IXZGF_L 16 chr21 23094798 255 13M1I18M * 0 0 GCAAGCTCCACTTCCCGGGTTCACGCCATTCT *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	367 F2YP0BU02IODR5_L 0 chr21 30935325 255 37M * 0 0 GAAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCA *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	368 F2YP0BU02IMZBL_L 16 chr21 31603486 255 28M1D1M * 0 0 ATACAAAAATTAGCCGGGCACAGTGGCAG *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	369 F2YP0BU02JA9PR_L 16 chr21 31677159 255 23M * 0 0 CACACCTGTAACCCCAGCACTTT *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	370 F2YP0BU02HKC61_R 0 chr21 31678718 255 40M * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	371 F2YP0BU02HKC61_R 0 chr21 31678718 255 40M * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	372 F2YP0BU02HVA88 16 chr21 31703558 255 1M1D35M8S * 0 0 TGGGATTACAGGCGTGAGCTACCACACCCAGCCAGAgttcaaat *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	373 F2YP0BU02JDCF1_L 0 chr21 31816600 255 38M * 0 0 AGGAGAATCGCTTGAACCCAGGAGGCAGAGGTTGCGGT *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	374 F2YP0BU02GZ1GO_R 0 chr21 33360122 255 6S38M * 0 0 cctagaCTTCACACACACACACACACACACACACACACACACAC *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	375 F2YP0BU02FX387_L 16 chr22 14786201 255 26M * 0 0 TGGATGAAGCTGGAAACCATCATTCT *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	376 F2YP0BU02IF2NE_R 0 chr22 16960842 255 40M10S * 0 0 TGGCATGCACCTGTAGTCTCAGCTACTTGGGAGGCTGAGGtgggaggatc *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	377 F2YP0BU02F4TVA 0 chr22 19200522 255 49M * 0 0 CCTGGGAGGCGGAGGTTGCAGTGAGCCGAGATCACGCCATTGCACTCCA *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	378 F2YP0BU02HKC61_R 16 chr22 29516998 255 8S32M * 0 0 agacagagTCTTGCTTTGTCACCCAGGCTGGAGTGCAGTG *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	379 F2YP0BU02FS4EM_R 0 chr22 30159364 255 29M * 0 0 CTCCTGCCTCAGCCTCCCGAGTAGTTGGG *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	380 F2YP0BU02G197P_L 0 chr22 32044496 255 40M10S * 0 0 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTgaataatgcc *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	381 F2YP0BU02FIING 16 chr22 45959944 255 3M1I11M1I26M * 0 0 AGCTATGGTACTGGCTATGAAAGCAGACACATAGACCAATGG *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	382 F2YP0BU02GUB9L_L 16 chr22 49198404 255 16M1I20M * 0 0 CACCACGCTCGGCTAATTTTTGTATTTTTAGTAGAGA *
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	383
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	384 The user must provide a mapping file (which might better be called an unmapping file). This file is usually
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	385 created by split_paired_reads, and tells us how to map the subsegments back to original coordinates in a single
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	386 read (this means the left and right mates were part of a single read). The mapping file contains four columns.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	387 The first two give the mates's name (including the suffix) and the read name. The last two columns describe how
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	388 much of the full original sequence is missing from the mate. For example, in the read below, the left mate is
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	389 missing 63 on the right (42 for the linker and 21 for the right half). The right mate is missing 339 on the left.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	390
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	391 left half: TTTCAACATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCA
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	392 AAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTTCGGC
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	393 AAAATTCAACAAAACTCCATGCTAAAACTCTCAATAAGGTATTGATGGGA
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	394 CATGCCGCATAATAATAAGACATATCTATGACAAACCCACAGCCAATATC
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	395 ATGCTGAATGCACAAAAATTGGAAGCATTCCCTTTGAAAACTGGCACAAG
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	396 ACTGGGATGCCCTCTCTCACAACTCCTATTCAACATAGTGTTGGAAG
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	397 linker: CGTAATAACTTCGTATAGCATACATTATACGAAGTCATACGA
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	398 right half: CTCCTGCCTCAGCCTCCCGAG
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	399
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	400 mate_name read_name offset_to_start offset_from_end
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	401 F2YP0BU02FS4EM_L F2YP0BU02FS4EM 0 71
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	402 F2YP0BU02FS4EM_R F2YP0BU02FS4EM 339 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	403
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	404 The user can also specify a quality scores file, which should look something like this. Quality values are presumed
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	405 to be PHRED scores, written in space-delimited decimal.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	406
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	407 >F2YP0BU02FS4EM
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	408 38 38 38 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 38 21 21 21 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	409 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 33
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	410 32 32 40 40 40 21 21 18 18 21 34 34 31 40 40 40 40 40 40 40 40 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	411 40 40 40 40 40 40 40 40 40 40 40 32 32 32 32 40 40 40 40 40 40 40 34 34 35
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	412 31 31 28 28 33 33 33 36 36 36 17 17 17 19 26 36 36 36 40 40 40 40 40 33 34
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	413 34 34 39 39 39 40 40 40 40 40 33 33 34 34 40 40 40 40 40 40 40 39 39 39 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	414 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	415 40 40 40 40 40 40 40 39 39 39 39 39 39 40 40 40 39 39 39 40 40 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	416 40 40 40 40 40 40 40 40 40 40 40 40 40 26 26 26 26 26 40 40 38 38 37 35 33
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	417 36 40 19 17 17 17 17 19 19 23 30 20 20 20 23 35 40 36 36 36 36 36 36 36 36
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	418 39 40 34 20 27 27 35 39 40 37 40 40 40 40 40 40 40 40 40 40 34 34 35 39 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	419 40 40 40 40 40 40 39 39 39 40 40 40 40 36 36 32 32 28 28 29 30 36 40 30 26
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	420 26 26 34 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	421 40 39 35 34 34 40 40 40 40 30 30 30 35 40 40 40 40 40 39 39 36 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	422 39 39 39 39 30 30 28 35 35 39 40 40 40 40 40 35 35 35
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	423 >F2YP0BU02G197P
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	424 40 40 40 40 40 40 40 40 40 40 39 39 39 39 39 39 40 40 40 40 40 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	425 40 40 40 40 26 26 26 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	426 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	427 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	428 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 34 34 34 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	429 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	430 40 40 40 40 40 40 40 34 34 34 34 40 40 40 40 34 34 34 34 40 40 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	431 40 40 40 40 40 39 39 39 34 34 34 34 40 40 40 40 39 39 25 25 26 39 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	432 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	433 33 33 33 33 40 35 21 21 21 30 38 40 40 40 40 40 40 40 40 35 35 30 30 30 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	434 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	435 40 40 40 40 40 40 40 40 40 40 40 40 39 39 39 40 40 40 40 40 40 40 40 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	436 40 40 40 39 39 39 40 40
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	437 >F2YP0BU02FIING
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	438 32 32 32 25 25 25 25 24 25 30 31 30 27 27 27 28 28 21 19 19 13 13 13 14 19
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	439 19 17 19 16 16 25 28 22 21 17 17 18 25 24 25 25 25
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	440
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	441 The output file is also SAM:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	442
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	443 (SAM header lines omitted)
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	444 F2YP0BU02G7LK5 81 chr21 15557360 255 40M303H * 0 0 ATTTTATTCTCTTTGAAGCAATTGTGAATGGGAGTTTACT D>>>>IIIIIIHHG???IIIIIIIIIHHHFFEIH999HII
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	445 F2YP0BU02HXV58 145 chr21 15952091 255 226H40M6S * 0 0 GCAAATTGTGCTGCTTTAAACATGCGTGTGCAAGTATCTTtttcat AA===DDDDAAAAD???:::ABBBBBAAA:888ECF;F>>>?8??@
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	446 F2YP0BU02HREML 65 chr21 16386077 255 320H33M5S * 0 0 CCAAAGTTCTGGGATTACAGGCGTGAGCCATCGcgccc HH???HHIIIHFHIIIIIIICDDHHIIIIIIHHHHHHH
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	447 F2YP0BU02IOF1F 129 chr21 17567321 255 7S28M409H * 0 0 taaagagAAGAATTCTCAACCCAGAATTTCATATC 4100<<A>4113:<EFGGGFFFHHHHHHDFFFFED
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	448 F2YP0BU02IKX84 81 chr21 18491628 255 22M1D18M9S341H * 0 0 GTCTCTACCAAAAAATACAAAAATTAGCCGGGCGTGGTGGcatgtctgt ;;;=7@.55------?2?11112GGB=CCCCDIIIIIIIIIHHHHHHII
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	449 F2YP0BU02GW5VA 145 chr21 20255344 255 286H6S32M * 0 0 caagaaCAAACACATTCAAAAGCTAGTAGAAGGCAAGA IIIIIIIHHHIIIIIIICCCCIIIIIIIIIIIIIIIII
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	450 F2YP0BU02JIMJ4 65 chr21 22383051 255 208H19M * 0 0 CCCTTTATCATTTTTTATT 555544E?GE113344I22
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	451 F2YP0BU02IXZGF 145 chr21 23094798 255 291H13M1I18M * 0 0 GCAAGCTCCACTTCCCGGGTTCACGCCATTCT IIIIIIIIIIIGG;;;GGHIIIIIGGGIIIII
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	452 F2YP0BU02IODR5 129 chr21 30935325 255 37M154H * 0 0 GAAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCA 6...7/--..,30;9<<>@BFFFAAAAHIIIIIH@@@
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	453 F2YP0BU02IMZBL 145 chr21 31603486 255 342H28M1D1M * 0 0 ATACAAAAATTAGCCGGGCACAGTGGCAG BB1552222<<>9==8;;?AA=??A???A
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	454 F2YP0BU02JA9PR 145 chr21 31677159 255 229H23M * 0 0 CACACCTGTAACCCCAGCACTTT IIIIIIIIIIICCCCIIIIIHHH
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	455 F2YP0BU02HKC61 65 chr21 31678718 255 300H40M * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT AA@BD:::==AAA@A?8888:<90004<>>?><<<<4442
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	456 F2YP0BU02HKC61 65 chr21 31678718 255 300H40M * 0 0 CACTGCACTCCAGCCTGGGTGACAAAGCAAGACTCTGTCT AA@BD:::==AAA@A?8888:<90004<>>?><<<<4442
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	457 F2YP0BU02HVA88 16 chr21 31703558 255 1M1D35M8S * 0 0 TGGGATTACAGGCGTGAGCTACCACACCCAGCCAGAgttcaaat >8888DFFHHGFHHHH@@?@?DDC96666HIIIFFFFFFFFFFF
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	458 F2YP0BU02JDCF1 129 chr21 31816600 255 38M103H * 0 0 AGGAGAATCGCTTGAACCCAGGAGGCAGAGGTTGCGGT IIIIIIIIIIIHHHIIHHHIIIIIIIIIIIIIIIIIII
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	459 F2YP0BU02GZ1GO 65 chr21 33360122 255 76H6S38M * 0 0 cctagaCTTCACACACACACACACACACACACACACACACACAC BBBBD?:688CFFFFFFFFFFFFFFFFFFFFFFFFFFDDBBB51
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	460 F2YP0BU02FX387 145 chr22 14786201 255 201H26M * 0 0 TGGATGAAGCTGGAAACCATCATTCT IIHHHHHHHHHHHHHFFFFFFFFFFF
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	461 F2YP0BU02IF2NE 65 chr22 16960842 255 209H40M10S * 0 0 TGGCATGCACCTGTAGTCTCAGCTACTTGGGAGGCTGAGGtgggaggatc BAAADDDDFDDDDDDBBA889<A?4444000@<>AA?9444;;8>77<7-
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	462 F2YP0BU02F4TVA 0 chr22 19200522 255 49M * 0 0 CCTGGGAGGCGGAGGTTGCAGTGAGCCGAGATCACGCCATTGCACTCCA FFF???FFFFFIIIIIIIIIIIIIIIIIIIIIIIHHIIFHFFFGDDB=5
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	463 F2YP0BU02HKC61 81 chr22 29516998 255 8S32M300H * 0 0 agacagagTCTTGCTTTGTCACCCAGGCTGGAGTGCAGTG 2444<<<<>?>><40009<:8888?A@AAA==:::DB@AA
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	464 F2YP0BU02FS4EM 65 chr22 30159364 255 339H29M * 0 0 CTCCTGCCTCAGCCTCCCGAGTAGTTGGG IIIIHHEIIIIHHHH??=DDHIIIIIDDD
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	465 F2YP0BU02G197P 129 chr22 32044496 255 40M10S258H * 0 0 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTgaataatgcc IIIIIIIIIIHHHHHHIIIIIIIIIIIII;;;IIIIIIIIIIIIIIIIII
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	466 F2YP0BU02FIING 16 chr22 45959944 255 3M1I11M1I26M * 0 0 AGCTATGGTACTGGCTATGAAAGCAGACACATAGACCAATGG :::9:32267=:114244/...446==<<<?@?:9::::AAA
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	467 F2YP0BU02GUB9L 145 chr22 49198404 255 176H16M1I20M * 0 0 CACCACGCTCGGCTAATTTTTGTATTTTTAGTAGAGA IIIIIIIIIHAAC;<</////@4F5778;IIIIIIII
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	468
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	469 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	470 left_suffix = "_L"
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	471 right_suffix = "_R"
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	472 # Read the mapping
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	473 mate_to_read_dict = {}
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	474 i = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	475 for i, line in enumerate( file( tmp_mates_mapping_file_name, 'rb' ) ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	476 line = line.strip()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	477 if not line.startswith( "#" ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	478 fields = line.split()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	479 if len( fields ) != 4:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	480 skip_line( "num_fields", i+1, line )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	481 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	482 mate_name, read_name, s_offset, e_offset = fields
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	483 if mate_name in mate_to_read_dict:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	484 skip_line( 'two_mate_names', i+1, mate_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	485 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	486 mate_to_read_dict[ mate_name ] = ( read_name, int( s_offset ), int( e_offset ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	487 # Read sequence data
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	488 read_to_nucs_dict = {}
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	489 seqs = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	490 fasta_reader = FastaReader( file( input2, 'rb' ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	491 while True:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	492 seq = fasta_reader.next()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	493 if not seq:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	494 break
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	495 seqs += 1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	496 seq_text_upper = seq.text.upper()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	497 if seq.name in read_to_nucs_dict:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	498 if seq_text_upper != read_to_nucs_dict[ seq.name ]:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	499 skip_line( 'inconsistent_reads', seqs, seq.name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	500 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	501 read_to_nucs_dict[ seq.name ] = seq_text_upper
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	502 # Read quality data
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	503 def quality_sequences( f ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	504 seq_name = None
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	505 seq_quals = None
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	506 line_number = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	507 for line in f:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	508 line_number += 1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	509 line = line.strip()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	510 if line.startswith( ">" ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	511 if seq_name != None:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	512 yield ( seq_name, seq_quals, seq_line )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	513 seq_name = sequence_name( line )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	514 seq_line = line_number
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	515 seq_quals = []
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	516 elif seq_name is None:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	517 skip_line( 'no_header', line_number, line )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	518 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	519 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	520 seq_quals += [ int( q ) for q in line.split() ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	521 if seq_name is not None:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	522 yield ( seq_name, seq_quals, seq_line )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	523 def sequence_name( s ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	524 s = s[ 1: ].strip()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	525 if not s:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	526 return ""
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	527 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	528 return s.split()[ 0 ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	529 read_to_quals_dict = {}
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	530 # TODO: should we use Dan's fastaNamedReader here?
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	531 for seq_name, quals, line_number in quality_sequences( file( input4 ) ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	532 quals = samify_phred_scores( quals )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	533 if seq_name in read_to_quals_dict:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	534 if quals != read_to_quals_dict[ seq_name ]:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	535 skip_line( 'inconsistent_reads', line_number, seq_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	536 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	537 if len( quals ) != len( read_to_nucs_dict[ seq_name ] ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	538 skip_line( 'inconsistent_read_lengths', line_number, seq_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	539 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	540 read_to_quals_dict[ seq_name ] = quals
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	541 # process the SAM file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	542 tmp_align_file_names = ' '.join( tmp_align_file_name_list )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	543 combined_chrom_file_name = get_tmp_file_name( suffix='combined_chrom' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	544 command = 'cat %s \| grep -v "^@" \| sort -k 1 > %s' % ( tmp_align_file_names, combined_chrom_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	545 run_command( command )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	546 fout = file( output, 'w+b' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	547 has_non_header = False
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	548 i = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	549 for i, line in enumerate( file( combined_chrom_file_name, 'rb' ) ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	550 line = line.strip()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	551 if line.startswith( "@" ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	552 if has_non_header:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	553 skip_line( 'sam_headers', i+1, line )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	554 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	555 fout.write( "%s\n" % line )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	556 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	557 has_non_header = True
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	558 fields = line.split()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	559 num_fields = len( fields )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	560 if num_fields < SAM_MIN_COLUMNS:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	561 skip_line( 'sam_min_columns', i+1, line )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	562 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	563 # Set flags for mates
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	564 try:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	565 flag = int( fields[ SAM_FLAG_COLUMN ] )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	566 except ValueError:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	567 skip_line( 'sam_flag', i+1, line )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	568 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	569 if not( flag & ( BAM_FPAIRED + BAM_FREAD1 + BAM_FREAD2 ) == 0 ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	570 skip_line( 'reads_paired', i+1, line )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	571 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	572 mate_name = fields[ SAM_QNAME_COLUMN ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	573 unmap_it = False
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	574 half = None
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	575 if mate_name.endswith( left_suffix ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	576 flag += BAM_FPAIRED + BAM_FREAD2
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	577 fields[ SAM_FLAG_COLUMN ] = "%d" % flag
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	578 unmap_it = True
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	579 half = "L"
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	580 elif mate_name.endswith( right_suffix ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	581 flag += BAM_FPAIRED + BAM_FREAD1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	582 fields[ SAM_FLAG_COLUMN ] = "%d" % flag
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	583 unmap_it = True
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	584 half = "R"
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	585 on_plus_strand = ( flag & BAM_FREVERSE == 0 )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	586 # Convert position from mate to read by adding clipping to cigar
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	587 if not unmap_it:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	588 read_name = mate_name
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	589 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	590 try:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	591 read_name, s_offset, e_offset = mate_to_read_dict[ mate_name ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	592 except KeyError:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	593 skip_line( 'missing_mate', i+1, mate_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	594 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	595 cigar = fields[ SAM_CIGAR_COLUMN ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	596 cigar_prefix = None
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	597 cigar_suffix = None
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	598 if half == "L":
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	599 if on_plus_strand:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	600 if s_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	601 cigar_prefix = ( s_offset, "S" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	602 if e_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	603 cigar_suffix = ( e_offset, "H" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	604 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	605 if e_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	606 cigar_prefix = ( e_offset, "H" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	607 if s_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	608 cigar_suffix = ( s_offset, "S" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	609 elif half == "R":
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	610 if on_plus_strand:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	611 if s_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	612 cigar_prefix = ( s_offset, "H" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	613 if e_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	614 cigar_suffix = ( e_offset, "S" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	615 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	616 if e_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	617 cigar_prefix = ( e_offset, "S" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	618 if s_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	619 cigar_suffix = ( s_offset, "H" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	620 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	621 if on_plus_strand:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	622 if s_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	623 cigar_prefix = ( s_offset, "S" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	624 if e_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	625 cigar_suffix = ( e_offset, "S" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	626 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	627 if e_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	628 cigar_prefix = ( e_offset, "S" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	629 if s_offset > 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	630 cigar_suffix = ( s_offset, "S" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	631 if cigar_prefix != None:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	632 count, op = cigar_prefix
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	633 cigar = prefix_cigar( "%d%s" % ( count, op ), cigar )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	634 if op == "S":
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	635 refPos = int( fields[ SAM_POS_COLUMN ] ) - count
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	636 fields[ SAM_POS_COLUMN ] = "%d" % refPos
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	637 if cigar_suffix != None:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	638 count, op = cigar_suffix
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	639 cigar = suffix_cigar( cigar,"%d%s" % ( count, op) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	640 fields[ SAM_QNAME_COLUMN ] = read_name
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	641 fields[ SAM_CIGAR_COLUMN ] = cigar
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	642 # Fetch sequence and quality values, and flip/clip them
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	643 if read_name not in read_to_nucs_dict:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	644 skip_line( 'missing_seq', i+1, read_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	645 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	646 nucs = read_to_nucs_dict[ read_name ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	647 if not on_plus_strand:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	648 nucs = reverse_complement( nucs )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	649 quals = None
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	650 if read_to_quals_dict != None:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	651 if read_name not in read_to_quals_dict:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	652 skip_line( 'missing_quals', i+1, read_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	653 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	654 quals = read_to_quals_dict[ read_name ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	655 if not on_plus_strand:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	656 quals = reverse_string( quals )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	657 cigar = split_cigar( fields[ SAM_CIGAR_COLUMN ] )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	658 nucs, quals = clip_for_cigar( cigar, nucs, quals )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	659 fields[ SAM_SEQ_COLUMN ] = nucs
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	660 if quals != None:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	661 fields[ SAM_QUAL_COLUMN ] = quals
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	662 # Output the line
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	663 fout.write( "%s\n" % "\t".join( fields ) )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	664 fout.close()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	665
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	666 def prefix_cigar( prefix, cigar ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	667 ix = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	668 while cigar[ ix ].isdigit():
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	669 ix += 1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	670 if cigar[ ix ] != prefix[ -1 ]:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	671 return prefix + cigar
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	672 count = int( prefix[ :-1 ] ) + int( cigar[ :ix ] )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	673 return "%d%s%s" % ( count, prefix[ -1 ], cigar[ ix+1: ] )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	674
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	675 def suffix_cigar( cigar, suffix ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	676 if cigar[ -1 ] != suffix[ -1 ]:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	677 return cigar + suffix
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	678 ix = len( cigar ) - 2
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	679 while cigar[ix].isdigit():
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	680 ix -= 1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	681 ix += 1
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	682 count = int( cigar[ ix:-1 ] ) + int( suffix[ :-1 ] )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	683 return "%s%d%s" % ( cigar[ :ix ], count, suffix[ -1 ] )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	684
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	685 def split_cigar( text ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	686 fields = []
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	687 field = []
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	688 for ch in text:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	689 if ch not in "MIDHS":
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	690 field += ch
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	691 continue
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	692 if field == []:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	693 raise ValueError
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	694 fields += [ ( int( "".join( field ) ), ch ) ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	695 field = []
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	696 if field != []:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	697 raise ValueError
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	698 return fields
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	699
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	700 def clip_for_cigar( cigar, nucs, quals ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	701 # Hard clip prefix
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	702 count, op = cigar[0]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	703 if op == "H":
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	704 nucs = nucs[ count: ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	705 if quals != None:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	706 quals = quals[ count: ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	707 count, op = cigar[ 1 ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	708 # Soft clip prefix
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	709 if op == "S":
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	710 nucs = nucs[ :count ].lower() + nucs[ count: ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	711 # Hard clip suffix
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	712 count,op = cigar[ -1 ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	713 if op == "H":
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	714 nucs = nucs[ :-count ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	715 if quals != None:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	716 quals = quals[ :-count ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	717 count, op = cigar[ -2 ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	718 # Soft clip suffix
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	719 if op == "S":
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	720 nucs = nucs[ :-count ] + nucs[ -count: ].lower()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	721 return nucs, quals
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	722
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	723 def samify_phred_scores( quals ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	724 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	725 Convert a decimal list of phred base-quality scores to a sam quality string.
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	726 Note that if a quality is outside the dynamic range of sam's ability to
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	727 represent it, we clip the value to the max allowed. SAM quality scores
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	728 range from chr(33) to chr(126).
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	729 """
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	730 if min( quals ) >= 0 and max( quals ) <= 126-33:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	731 return "".join( [ chr( 33 + q ) for q in quals ] )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	732 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	733 return "".join( [ chr( max( 33, min( 126, 33+q ) ) ) for q in quals ] )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	734
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	735 def reverse_complement( nucs ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	736 complementMap = maketrans( "ACGTacgt", "TGCAtgca" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	737 return nucs[ ::-1 ].translate( complementMap )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	738
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	739 def reverse_string( s ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	740 return s[ ::-1 ]
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	741
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	742 def __main__():
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	743 # Parse command line
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	744 # input1: a reference genome ( 2bit or fasta )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	745 # input2: a collection of 454 paired end reads ( a fasta file )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	746 # input3: a linker sequence ( a very small fasta file )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	747 # input4: a base quality score 454 file ( qual454 )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	748 parser = optparse.OptionParser()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	749 parser.add_option( '', '--ref_name', dest='ref_name', help='The reference name to change all output matches to' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	750 parser.add_option( '', '--ref_source', dest='ref_source', help='The reference is cached or from the history' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	751 parser.add_option( '', '--ref_sequences', dest='ref_sequences', help='Number of sequences in the reference dataset' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	752 parser.add_option( '', '--source_select', dest='source_select', help='Use pre-set or cached reference file' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	753 parser.add_option( '', '--input1', dest='input1', help='The name of the reference file if using history or reference base name if using cached' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	754 parser.add_option( '', '--input2', dest='input2', help='The 454 reads file to align' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	755 parser.add_option( '', '--input3', dest='input3', help='The sequencing linker file' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	756 parser.add_option( '', '--input4', dest='input4', help='The base quality score 454 file' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	757 parser.add_option( '', '--output', dest='output', help='The output file' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	758 parser.add_option( '', '--lastz_seqs_file_dir', dest='lastz_seqs_file_dir', help='Directory of local lastz_seqs.loc file' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	759 ( options, args ) = parser.parse_args()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	760
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	761 # output version # of tool
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	762 try:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	763 tmp = tempfile.NamedTemporaryFile().name
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	764 tmp_stdout = open( tmp, 'wb' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	765 proc = subprocess.Popen( args='lastz -v', shell=True, stdout=tmp_stdout )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	766 tmp_stdout.close()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	767 returncode = proc.wait()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	768 stdout = None
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	769 for line in open( tmp_stdout.name, 'rb' ):
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	770 if line.lower().find( 'version' ) >= 0:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	771 stdout = line.strip()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	772 break
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	773 if stdout:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	774 sys.stdout.write( '%s\n' % stdout )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	775 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	776 raise Exception
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	777 except:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	778 sys.stdout.write( 'Could not determine Lastz version\n' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	779
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	780 if options.ref_name:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	781 ref_name = '[nickname=%s]' % options.ref_name
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	782 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	783 ref_name = ''
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	784 if options.ref_source == 'history':
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	785 # Reference is a fasta dataset from the history
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	786 try:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	787 # Ensure there is at least 1 sequence in the dataset ( this may not be necessary ).
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	788 error_msg = "The reference dataset is missing metadata, click the pencil icon in the history item and 'auto-detect' the metadata attributes."
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	789 ref_sequences = int( options.ref_sequences )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	790 if ref_sequences < 1:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	791 stop_err( error_msg )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	792 except:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	793 stop_err( error_msg )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	794 else:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	795 ref_sequences = 0
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	796 tmp_w12_name = get_tmp_file_name( suffix='vs_linker.W12' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	797 tmp_T1_name = get_tmp_file_name( suffix='vs_linker.T1' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	798 # Run lastz twice ( with different options ) on the linker sequence and paired end reads,
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	799 # looking for the linker ( each run finds some the other doesn't )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	800 command = 'lastz %s %s W=12 --notrans --exact=18 --match=1,3 O=1 E=3 Y=10 L=18 --ambiguousn --coverage=85 --format=general-:name2,zstart2+,length2,size2 > %s' % \
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	801 ( options.input3, options.input2, tmp_w12_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	802 run_command( command )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	803 command = 'lastz %s %s T=1 --match=1,2 O=1 E=2 X=15 K=10 Y=15 L=18 --ambiguousn --coverage=85 --format=general-:name2,zstart2+,length2,size2 > %s' % \
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	804 ( options.input3, options.input2, tmp_T1_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	805 run_command( command )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	806 # Combine the alignment output from the two lastz runs
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	807 tmp_combined_linker_file_name = get_tmp_file_name( suffix='vs_linker' )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	808 command = 'cat %s %s \| sort -u > %s' % ( tmp_w12_name, tmp_T1_name, tmp_combined_linker_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	809 run_command( command )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	810 # Use the alignment info to split reads into left and right mates
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	811 tmp_mates_mapping_file_name, tmp_mates_file_name, tmp_mates_short_file_name, tmp_mates_long_file_name = split_paired_reads( options.input2, tmp_combined_linker_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	812 # Align mates to the reference - tmp_align_file_names is a list of file names created by align_mates()
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	813 tmp_align_file_name_list = align_mates( options.input1, options.ref_source, ref_name, ref_sequences, tmp_mates_short_file_name, tmp_mates_long_file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	814 # Combine and convert mate coordinates back to read coordinates
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	815 paired_mate_unmapper( options.input2, options.input4, tmp_mates_mapping_file_name, tmp_align_file_name_list, options.output )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	816 # Delete all temporary files
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	817 for file_name in tmp_file_names:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	818 os.remove( file_name )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	819 # Handle any invalid lines in the input data
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	820 if total_skipped_lines:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	821 msgs = dict( bad_interval="Bad interval in line",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	822 inconsistent_read_lengths="Inconsistent read/quality lengths for seq #",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	823 inconsistent_reads="Inconsistent reads for seq #",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	824 inconsistent_sizes="Inconsistent sizes for seq #",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	825 missing_mate="Mapping file does not include mate on line",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	826 missing_quals="Missing quality values for name on line",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	827 missing_seq="Missing sequence for name on line",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	828 multiple_seqs="Multiple names for seq #",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	829 no_header="First quality sequence has no header",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	830 num_fields="Must have 4 fields in line",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	831 reads_paired="SAM flag indicates reads already paired on line",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	832 sam_flag="Bad SAM flag on line",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	833 sam_headers="SAM headers on line",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	834 sam_min_columns="Need 11 columns on line",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	835 two_mate_names="Mate name already seen, line",
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	836 wrong_seq_len="Size differs from length of seq #" )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	837 print "Skipped %d invalid lines: "
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	838 msg = ""
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	839 for k, v in skipped_lines.items():
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	840 if v[0]:
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	841 # v[0] is the number of times the error occurred
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	842 # v[1] is the position of the line or sequence in the file
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	843 # v[2] is the name of the sequence or the text of the line
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	844 msg += "(%d)%s %d:%s. " % ( v[0], msgs[k], v[1], v[2] )
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	845 print msg
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	846
643f8a898a36 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/lastz_paired_reads commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b devteam parents: diff changeset	847 if __name__=="__main__": __main__()

Mercurial > repos > devteam > lastz_paired_reads

annotate lastz_paired_reads_wrapper.py @ 0:643f8a898a36 draft default tip