Mercurial > repos > mvdbeek > r_goseq_1_22_0

changeset 6:0e9424413ab0 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit f95b47ed1a09ce14d3b565e8ea56d8bf12c35814-dirty
author mvdbeek
date Thu, 03 Mar 2016 09:56:51 -0500
parents b79c65c90744
children 9ffae7bc23c2
files get_length_and_gc_content.r get_length_and_gc_content.xml getgo.r getgo.xml go_macros.xml goseq.r goseq.xml test-data/category.tab test-data/dge_list.tab test-data/gc.tab test-data/gene_length.tab test-data/go_terms.tab test-data/in.fasta test-data/in.gtf test-data/length.tab test-data/wal.tab test-data/wall.tab
diffstat 16 files changed, 1260 insertions(+), 100 deletions(-) [+]
line wrap: on
line diff
--- a/get_length_and_gc_content.r	Sun Feb 28 11:52:10 2016 -0500
+++ b/get_length_and_gc_content.r	Thu Mar 03 09:56:51 2016 -0500
@@ -1,16 +1,23 @@
 # originally by Devon Ryan, https://www.biostars.org/p/84467/
-sink(stdout(), type = "message")
+
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 
-library(GenomicRanges)
-library(rtracklayer)
-library(Rsamtools)
-library(optparse)
-library(data.table)
+suppressPackageStartupMessages({
+    library("GenomicRanges")
+    library("rtracklayer")
+    library("Rsamtools")
+    library("optparse")
+    library("data.table")
+})
 
 option_list <- list(
     make_option(c("-g","--gtf"), type="character", help="Input GTF file with gene / exon information."),
     make_option(c("-f","--fasta"), type="character", default=FALSE, help="Fasta file that corresponds to the supplied GTF."),
-    make_option(c("-o","--output"), type="character", default=FALSE, help="Output file with gene name, length and GC content.")
+    make_option(c("-l","--length"), type="character", default=FALSE, help="Output file with gene name and length."),
+    make_option(c("-gc","--gc_content"), type="character", default=FALSE, help="Output file with gene name and GC content.")
   )
 
 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
@@ -18,7 +25,8 @@
 
 GTFfile = args$gtf
 FASTAfile = args$fasta
-output_file = args$output
+length = args$length
+gc_content = args$gc_content
 
 #Load the annotation and reduce it
 GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon")
@@ -41,9 +49,11 @@
     c(width, nGCs/width)
 }
 output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length))
-output <- setDT(data.frame(output), keep.rownames = TRUE)[]
-colnames(output) <- c("#gene_id", "length", "GC")
+output <- data.frame(setDT(data.frame(output), keep.rownames = TRUE)[])
+
 
-write.table(output, file=output_file, row.names=FALSE, quote=FALSE, sep="\t")
+write.table(output[,c(1,2)], file=length, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
+write.table(output[,c(1,3)], file=gc_content, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
+
 
 sessionInfo()
\ No newline at end of file
--- a/get_length_and_gc_content.xml	Sun Feb 28 11:52:10 2016 -0500
+++ b/get_length_and_gc_content.xml	Thu Mar 03 09:56:51 2016 -0500
@@ -1,9 +1,10 @@
-<tool id="length_and_gc_content" name="gene length and gc content from gtf file" version="0.1.0">
-    <description />
-    <requirements>
-        <requirement type="package" version="3.2.1">R</requirement>
-        <requirement type="package" version="1.22.0">goseq</requirement>
-    </requirements>
+<tool id="length_and_gc_content" name="gene length and gc content" version="0.1.0">
+    <description>from GTF file</description>
+    <macros>
+        <import>go_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command interpreter="Rscript">
         get_length_and_gc_content.r --gtf "$gtf"
         #if $fastaSource.genomeSource == "indexed":
@@ -11,10 +12,11 @@
         #else:
             --fasta "$fastaSource.fasta_history"
         #end if
-        --output "$output"
+        --length "$length"
+        --gc_content "$gc_content"
     </command>
     <inputs>
-        <param help="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" />
+        <param help="The GTF must match the FASTA file" label="GTF file for length and GC calculation" name="gtf" type="data" format="gtf" />
         <conditional name="fastaSource">
             <param help="choose history if you don't see the correct genome fasta" label="Select a reference fasta from your history or use a built-in fasta?" name="genomeSource" type="select">
                 <option value="indexed">Use a built-in fasta</option>
@@ -26,19 +28,40 @@
             </param>
         </when>
         <when value="history">
-            <param format="fasta" label="Select a fasta file, to serve as index reference" name="fasta_history" type="data" />
+            <param format="fasta" label="Select a fasta file that matches the supplied GTF file" name="fasta_history" type="data" />
         </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="tabular" label="length and gc content" name="output" />
+        <data format="tabular" label="gene length" name="length">
+            <!-- future: set this when 16.04 has been released
+            <actions>
+                <action name="column_names" type="metadata" default="gene,length" />
+            </actions>
+            -->
+        </data>
+        <data format="tabular" label="gene gc content" name="gc_content">
+            <!-- future: set this when 16.04 has been released
+             <actions>
+                <action name="column_names" type="metadata" default="gene,gc_content" />
+            </actions>
+            -->
+        </data>
     </outputs>
-    <tests></tests>
+    <tests>
+        <test>
+            <param name="gtf" value="in.gtf" ftype="gtf"></param>
+            <param name="fastaSource|genomeSource" value="history"></param>
+            <param name="fastaSource|fasta_history" value="in.fasta" ftype="fasta"></param>
+            <output name="length" file="length.tab"></output>
+            <output name="gc_content" file="gc.tab"></output>
+        </test>
+    </tests>
     <help>
 
         **What it does**
 
-        Returns a tabular file with gene name, length and GC content, based on a supplied GTF and a FASTA file.
+        Returns a tabular file with gene id and length and a tabular file with gene id and GC content, based on a supplied GTF and a FASTA file.
 
 
         </help>
--- a/getgo.r	Sun Feb 28 11:52:10 2016 -0500
+++ b/getgo.r	Thu Mar 03 09:56:51 2016 -0500
@@ -1,7 +1,15 @@
-suppressWarnings(suppressMessages(library(goseq)))
-suppressWarnings(suppressMessages(library(optparse)))
-suppressWarnings(suppressMessages(library(rtracklayer)))
-suppressWarnings(suppressMessages(library(reshape2)))
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+suppressPackageStartupMessages({
+    library("goseq")
+    library("optparse")
+    library("rtracklayer")
+    library("reshape2")
+})
+
 sink(stdout(), type = "message")
 
 option_list <- list(
@@ -15,21 +23,19 @@
 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
 args = parse_args(parser)
 
-# Vars:
+# vars
 
 gtf = args$gtf
 genome = args$genome
 gene_id = args$gene_id
 output = args$output
 cats = unlist(strsplit(args$cats, ','))
+
+# retrieve and transform data
 genes = unique(import.gff(gtf)$gene_id)
-go_categories = getgo(genes, genome, id, fetch.cats=cats)
-
-# transform go category list to sth. more manipulatable in galaxy
-go_categories <- lapply(go_categories, unlist)
+go_categories = getgo(genes, genome, gene_id, fetch.cats=cats)
 go_categories = goseq:::reversemapping(go_categories)
 go_categories = melt(go_categories)
-colnames(go_categories) = c("#gene_id", "go_category")
 
-write.table(go_categories, output, sep="\t", row.names = FALSE, quote = FALSE)
+write.table(go_categories, output, sep="\t", col.names = FALSE, row.names = FALSE, quote = FALSE)
 sessionInfo()
\ No newline at end of file
--- a/getgo.xml	Sun Feb 28 11:52:10 2016 -0500
+++ b/getgo.xml	Thu Mar 03 09:56:51 2016 -0500
@@ -1,9 +1,10 @@
-<tool id="getgo" name="Retrieve GO ontologies" version="0.1.0">
-    <description />
-    <requirements>
-        <requirement type="package" version="3.2.1">R</requirement>
-        <requirement type="package" version="1.22.0">goseq</requirement>
-    </requirements>
+<tool id="getgo" name="getgo" version="0.1.0">
+    <description>downloads gene ontologies for model organisms</description>
+    <macros>
+        <import>go_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command interpreter="Rscript">
         getgo.r --genome "$genome"
         --gtf "$gtf"
@@ -29,15 +30,24 @@
     <outputs>
         <data format="tabular" label="GO category mapping" name="output" />
     </outputs>
-    <tests></tests>
+    <tests>
+        <test>
+            <param name="gtf" value="in.gtf" ftype="gtf"></param>
+            <param name="genome" value="hg38"></param>
+            <param name="gene_id" value="ensGene"></param>
+            <param name="cats" value="GO:CC,GO:BP,GO:MF"></param>
+            <output name="output" file="go_terms.tab"></output>
+        </test>
+    </tests>
     <help>
 
         **What it does**
 
-        Returns a tabular file with GO gene categories.
+        Returns a tabular file with GO gene categories for all genes present in the input GTF file.
 
 
         </help>
     <citations>
+        <citation type="doi">10.1186/gb-2010-11-2-r14</citation>
     </citations>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/go_macros.xml	Thu Mar 03 09:56:51 2016 -0500
@@ -0,0 +1,24 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.2.1">R</requirement>
+            <requirement type="package" version="1.22.0">goseq</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <regex match="Execution halted"
+                   source="both"
+                   level="fatal"
+                   description="Execution halted." />
+            <regex match="Error in"
+                   source="both"
+                   level="fatal"
+                   description="An undefined error occured, please check your input carefully and contact your administrator." />
+            <regex match="Fatal error"
+                   source="both"
+                   level="fatal"
+                   description="An undefined error occured, please check your input carefully and contact your administrator." />
+        </stdio>
+    </xml>
+</macros>
\ No newline at end of file
--- a/goseq.r	Sun Feb 28 11:52:10 2016 -0500
+++ b/goseq.r	Thu Mar 03 09:56:51 2016 -0500
@@ -1,6 +1,12 @@
-sink(stdout(), type = "message")
-suppressWarnings(suppressMessages(library(goseq)))
-suppressWarnings(suppressMessages(library(optparse)))
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+suppressPackageStartupMessages({
+    library("goseq")
+    library("optparse")
+})
 
 option_list <- list(
     make_option(c("-d", "--dge_file"), type="character", help="Path to file with differential gene expression result"),
@@ -14,16 +20,20 @@
                 help="Genes with p.adjust below cutoff are considered not differentially expressed and serve as control genes"),
     make_option(c("-r", "--repcnt"), type="integer", default=100, help="Number of repeats for sampling"),
     make_option(c("-lf", "--length_file"), type="character", default="FALSE", help = "Path to tabular file mapping gene id to length"),
-    make_option(c("-g", "--genome"), type="character", help = "Genome [used for looking up correct gene length]"),
-    make_option(c("-i", "--gene_id"), type="character", help="Gene ID of gene column in DGE file"),
-    make_option(c("-cat", "--use_genes_without_cat"), default=FALSE, type="logical", help="A boolean to indicate whether genes without a categorie should still be used. For example, a large number of gene may have no GO term annotated.  If thisoption is set to FALSE, those genes will be ignored in the calculation of p-values(default behaviour).  If this option is set to TRUE, then these genes will count towards  the  total  number  of  genes  outside  the  category  being  tested  (default behaviour prior to version 1.15.2)."
-)
-  )
+    make_option(c("-cat_file", "--category_file"), default="FALSE", type="character", help = "Path to tabular file with gene_id <-> category mapping."),
+    make_option(c("-g", "--genome"), default=NULL, type="character", help = "Genome [used for looking up correct gene length]"),
+    make_option(c("-i", "--gene_id"), default=NULL, type="character", help = "Gene ID format of genes in DGE file"),
+    make_option(c("-cat", "--use_genes_without_cat"), default=FALSE, type="logical",
+                help="A large number of gene may have no GO term annotated. If this option is set to FALSE, genes without category will be ignored in the calculation of p-values(default behaviour). If TRUE these genes will count towards the total number of genes outside the tested category (default behaviour prior to version 1.15.2)."),
+    make_option(c("-plots", "--make_plots"), default=FALSE, type="logical", help="produce diagnostic plots?")
+    )
+
 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
 args = parse_args(parser)
 
 # Vars:
 dge_file = args$dge_file
+category_file = args$category_file
 p_adj_column = args$p_adj_colum
 p_adj_cutoff = args$p_adj_cutoff
 length_file = args$length_file
@@ -36,45 +46,72 @@
 sample_vs_wallenius_plot = args$sample_vs_wallenius_plot
 repcnt = args$repcnt
 use_genes_without_cat = args$use_genes_without_cat
+make_plots = args$make_plots
 
-# format DE genes into vector suitable for use with goseq
-dge_table = read.delim(dge_file, header = TRUE, sep="\t", check.names = FALSE)
+# format DE genes into named vector suitable for goseq
+first_line = read.delim(dge_file, header = FALSE, nrow=1)
+# check if header [character where numeric is expected]
+if (is.numeric(first_line[,p_adj_column])) {
+  dge_table = read.delim(dge_file, header = FALSE, sep="\t")
+  } else {
+  dge_table = read.delim(dge_file, header = TRUE, sep="\t")
+  }
+
 genes = as.integer(dge_table[,p_adj_column]<p_adj_cutoff)
 names(genes) = dge_table[,1] # Assuming first row contains gene names
 
-# Get gene lengths
+# gene lengths, assuming last column
 if (length_file != "FALSE" ) {
-  length_table = read.delim(length_file, header=TRUE, sep="\t", check.names=FALSE)
+  first_line = read.delim(dge_file, header = FALSE, nrow=1)
+  if (is.numeric(first_line[, ncol(first_line)])) {
+    length_table = read.delim(length_file, header=FALSE, sep="\t", check.names=FALSE)
+    } else {
+    length_table = read.delim(length_file, header=TRUE, sep="\t", check.names=FALSE)
+    }
   row.names(length_table) = length_table[,1]
-  gene_lengths = length_table[names(genes),]$length
+  gene_lengths = length_table[names(genes),][,ncol(length_table)]
   } else {
   gene_lengths = getlength(names(genes), genome, gene_id)
   }
 
 # Estimate PWF
 
-pdf(length_bias_plot)
-pwf=nullp(genes, genome, gene_id, gene_lengths)
-message = dev.off()
+if (make_plots == TRUE) {
+  pdf(length_bias_plot)
+}
+pwf=nullp(genes, genome = genome, id = gene_id, bias.data = gene_lengths, plot.fit=make_plots)
+graphics.off()
 
-# Fetch GO annotations:
-go_map=getgo(names(genes), genome, gene_id, fetch.cats=c("GO:CC", "GO:BP", "GO:MF", "KEGG"))
+# Fetch GO annotations if category_file hasn't been supplied:
+if (category_file == "FALSE") {
+  go_map=getgo(genes = names(genes), genome = genome, id = gene_id, fetch.cats=c("GO:CC", "GO:BP", "GO:MF", "KEGG"))
+  } else {
+  # check for header: first entry in first column must be present in genes, else it's a header
+  first_line = read.delim(category_file, header = FALSE, nrow=1)
+  if (first_line[,1] %in% names(genes)) {
+     go_map = read.delim(category_file, header = FALSE)
+     } else {
+     go_map = read.delim(category_file, header= TRUE)
+    }
+}
 
 # wallenius approximation of p-values
-GO.wall=goseq(pwf, genome, gene_id, use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
+GO.wall=goseq(pwf, genome = genome, id = gene_id, use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
 
-GO.nobias=goseq(pwf, genome, gene_id, method="Hypergeometric", use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
+GO.nobias=goseq(pwf, genome = genome, id = gene_id, method="Hypergeometric", use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
 
 # Sampling distribution
 if (repcnt > 0) {
-  GO.samp=goseq(pwf,genome, gene_id, method="Sampling", repcnt=repcnt, use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
+  GO.samp=goseq(pwf, genome = genome, id = gene_id, method="Sampling", repcnt=repcnt, use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
   # Compare sampling with wallenius
+  if (make_plots == TRUE) {
   pdf(sample_vs_wallenius_plot)
   plot(log10(GO.wall[,2]), log10(GO.samp[match(GO.samp[,1],GO.wall[,1]),2]),
      xlab="log10(Wallenius p-values)",ylab="log10(Sampling p-values)",
      xlim=c(-3,0))
      abline(0,1,col=3,lty=2)
-  message = dev.off()
+  graphics.off()
+  }
   write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE)
 }
 
--- a/goseq.xml	Sun Feb 28 11:52:10 2016 -0500
+++ b/goseq.xml	Thu Mar 03 09:56:51 2016 -0500
@@ -1,18 +1,16 @@
-<tool id="goseq" name="goseq gene ontology analyser" version="0.1.5">
-    <description />
-    <requirements>
-        <requirement type="package" version="3.2.1">R</requirement>
-        <requirement type="package" version="1.22.0">goseq</requirement>
-    </requirements>
+<tool id="goseq" name="goseq" version="0.2.0">
+    <description>tests for overrepresented gene categories</description>
+    <macros>
+        <import>go_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
     <command interpreter="Rscript">
         goseq.r --dge_file "$dge_file"
         --p_adj_column "$p_adj_column"
         --cutoff "$p_adj_cutoff"
-        #if $source.use_length_file == "yes":
         --length_file "$length_file"
-        #end if
-        --genome "$genome"
-        --gene_id "$gene_id"
+        --category_file "$category_file"
         --wallenius_tab "$wallenius_tab"
         --sampling_tab "$sampling_tab"
         --nobias_tab "$nobias_tab"
@@ -20,36 +18,26 @@
         --sample_vs_wallenius_plot "$sample_vs_wallenius_plot"
         --repcnt "$repcnt"
         --use_genes_without_cat "$use_genes_without_cat"
+        --make_plots "$make_plots"
     </command>
     <inputs>
         <param help="deseq2/edger/limma differential gene expression list" label="DGE list" name="dge_file" type="data" format="tabular" />
         <param help="Select the column that contains the multiple-testing corrected p-value" label="p adjust column" name="p_adj_column" type="data_column" numeric="true" data_ref="dge_file"/>
-        <param help="A boolean to indicate whether genes without a categorie should still be used. For example, a large number of gene may have no GO term annotated.  If this option is set to FALSE, those genes will be ignored in the calculation of p-values. If this option is set to TRUE, then these genes will count towards the total number of genes outside the category being tested"
-               name="use_genes_without_cat" label="Count genes without any category" type="boolean"/>
+        <param label="Gene length file for length bias correction" help="You can calculate the gene length using the get length and gc content tool" name="length_file" type="data" format="tabular" required="true" />
+        <param label="Gene category file" help="You can obtain a mapping of gene id to gene ontology using the getgo tool" name="category_file" type="data" format="tabular" required="true" />
+        <param help="For example, a large number of gene may have no GO term annotated. If this option is set to FALSE, those genes will be ignored in the calculation of p-values. If this option is set to TRUE, then these genes will count towards the total number of genes outside the category being tested"
+               name="use_genes_without_cat" label="Count genes without any category?" type="boolean"/>
         <param help="Typically 0.05 after multiple testing correction" max="1" label="Minimum p adjust value to consider genes as differentially expressed" name="p_adj_cutoff" type="float" value="0.05" />
-        <conditional name="source">
-            <param help="This is needed if the gene length is not available in goseq. e.g. hg38 and mm10." label="Use gene length file?" name="use_length_file" type="select">
-                <option value="no">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="yes">
-                <param label="Gene length file" name="length_file" type="data" format="tabular" required="false" />
-            </when>
-            <when value="no">
-            </when>
-        </conditional>
-        <param help="Needed to retrieve gene length for length correction" label="Select the genome source" name="genome" size="3" type="select">
-            <options from_data_table="go_genomes"></options>
-        </param>
-        <param help="Needed for GO analysis" label="Select gene identifier" name="gene_id" type="select">
-            <options from_data_table="go_gene_ids"></options>
-        </param>
+        <param help="These plots may help you compare the different p-value estimation methods that goseq can use." label="Produce diagnostic plots?" name="make_plots" type="boolean"></param>
         <param help="Draw this many random control gene sets. Set to 0 to not do sampling. Larger values take a long time" label="sampling depth" name="repcnt" size="3" type="integer" min="0" max="10000" value="0" />
     </inputs>
     <outputs>
-        <data format="pdf" label="length bias plot" name="length_bias_plot" />
+        <data format="pdf" label="length bias plot" name="length_bias_plot">
+            <filter>make_plots</filter>
+        </data>
         <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot">
             <filter>repcnt != 0</filter>
+            <filter>make_plots</filter>
         </data>
         <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" />
         <data format="tabular" label="Ranked category list - sampling" name="sampling_tab">
@@ -60,21 +48,32 @@
     <tests>
         <test>
             <param name="dge_file" value="dge_list.tab" ftype="tabular"/>
-            <param name="use_length_file" value="no" />
+            <param name="length_file" value="gene_length.tab" ftype="tabular"/>
+            <param name="category_file" value="category.tab" ftype="tabular"/>
+            <param name="use_genes_without_cat" value="true" />
             <param name="p_adj_column" value="2" />
-            <param name="genome" value="hg19" />
-            <param name="gene_id" value="ensGene" />
-            <output name="wallenius_tab" file="wall.tab" compare="contains"/>/>
+            <output name="wallenius_tab" file="wal.tab" compare="contains"/>/>
         </test>
     </tests>
     <help>
 
         **What it does**
 
-        Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.
+        Detects Gene Ontology and/or other user defined categories which are over/under-represented in RNA-seq data.
 
         Options map closely to the excellent manual_
 
+
+        **Input files**
+
+        goseq needs information about the length of a gene to correct for potential length bias in differentially expressed genes.
+        The format of this file is tabular, with gene_id in the first column and length in the second column.
+        The "get length and gc content" tool can produce such a file.
+
+        You will also need a file describing the membership of genes in categories. The format of this file is gene_id in the first column,
+        category name in the second column. If you are interested in gene ontology categories you can use the getgo file to retrive
+        gene ontologies for model organisms, or you can construct your own file.
+
         .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf
 
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/category.tab	Thu Mar 03 09:56:51 2016 -0500
@@ -0,0 +1,6 @@
+ENSG00000162526	GO:0000003
+ENSG00000198648	GO:0000278
+ENSG00000112312	GO:0000278
+ENSG00000174442	GO:0000278
+ENSG00000108953	GO:0000278
+ENSG00000167842	GO:0000278
--- a/test-data/dge_list.tab	Sun Feb 28 11:52:10 2016 -0500
+++ b/test-data/dge_list.tab	Thu Mar 03 09:56:51 2016 -0500
@@ -1,4 +1,3 @@
-Name	adj.p.value
 ENSG00000140459	0.72654265501997
 ENSG00000236824	0.621241793648661
 ENSG00000162526	0.104072112354657
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gc.tab	Thu Mar 03 09:56:51 2016 -0500
@@ -0,0 +1,1 @@
+ENSG00000162526	0.388349514563107
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_length.tab	Thu Mar 03 09:56:51 2016 -0500
@@ -0,0 +1,948 @@
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+ENSG00000184481	3447
+ENSG00000184731	3968
+ENSG00000184831	2353
+ENSG00000185189	4924
+ENSG00000185238	5467
+ENSG00000185482	2096
+ENSG00000185504	5354
+ENSG00000185670	3348
+ENSG00000185798	1797
+ENSG00000185885	1080
+ENSG00000186056	4024
+ENSG00000186106	5820
+ENSG00000186130	4106
+ENSG00000186532	6777
+ENSG00000186583	2007
+ENSG00000186743	740
+ENSG00000187144	4506
+ENSG00000187172	4080
+ENSG00000187186	1833
+ENSG00000187187	9007
+ENSG00000187210	6463
+ENSG00000187504	746
+ENSG00000187605	12271
+ENSG00000187994	4201
+ENSG00000188021	4230
+ENSG00000188039	8495
+ENSG00000188206	5007
+ENSG00000188295	1980
+ENSG00000188529	10277
+ENSG00000188549	7510
+ENSG00000188738	23761
+ENSG00000188786	8024
+ENSG00000188997	4164
+ENSG00000189143	4702
+ENSG00000189221	5528
+ENSG00000189343	883
+ENSG00000196074	6466
+ENSG00000196119	1146
+ENSG00000196123	4780
+ENSG00000196263	6783
+ENSG00000196305	7401
+ENSG00000196357	3953
+ENSG00000196419	3288
+ENSG00000196507	2305
+ENSG00000196549	9620
+ENSG00000196632	11472
+ENSG00000196696	6114
+ENSG00000196739	13988
+ENSG00000196741	1253
+ENSG00000196747	503
+ENSG00000196812	1328
+ENSG00000197045	7966
+ENSG00000197062	2933
+ENSG00000197121	12761
+ENSG00000197128	6096
+ENSG00000197535	12988
+ENSG00000197744	327
+ENSG00000197888	2077
+ENSG00000197961	7251
+ENSG00000198046	8810
+ENSG00000198155	2804
+ENSG00000198198	17331
+ENSG00000198431	6708
+ENSG00000198464	4836
+ENSG00000198482	5432
+ENSG00000198515	3581
+ENSG00000198520	3166
+ENSG00000198648	4247
+ENSG00000198746	2225
+ENSG00000198752	7958
+ENSG00000198865	3431
+ENSG00000198929	7771
+ENSG00000198961	5217
+ENSG00000203441	872
+ENSG00000203616	333
+ENSG00000203668	7078
+ENSG00000203837	2354
+ENSG00000203865	2458
+ENSG00000203950	1265
+ENSG00000203995	4694
+ENSG00000204253	881
+ENSG00000204334	601
+ENSG00000204348	2483
+ENSG00000204385	3369
+ENSG00000204392	1077
+ENSG00000204394	6081
+ENSG00000204396	3638
+ENSG00000204628	5990
+ENSG00000204805	342
+ENSG00000204859	4503
+ENSG00000204956	6252
+ENSG00000205084	6015
+ENSG00000205208	3730
+ENSG00000205268	7425
+ENSG00000205485	3110
+ENSG00000205560	4102
+ENSG00000205628	3484
+ENSG00000206192	2978
+ENSG00000206560	11279
+ENSG00000210100	69
+ENSG00000210174	65
+ENSG00000211584	4921
+ENSG00000213033	1212
+ENSG00000213062	911
+ENSG00000213066	15159
+ENSG00000213077	2281
+ENSG00000213148	464
+ENSG00000213174	414
+ENSG00000213197	694
+ENSG00000213318	783
+ENSG00000213339	3430
+ENSG00000213493	1451
+ENSG00000213588	3014
+ENSG00000213711	814
+ENSG00000213742	5308
+ENSG00000213760	2147
+ENSG00000213793	551
+ENSG00000213864	676
+ENSG00000213880	797
+ENSG00000213904	4208
+ENSG00000213906	3233
+ENSG00000213917	815
+ENSG00000213971	5091
+ENSG00000214029	15455
+ENSG00000214174	3858
+ENSG00000214389	784
+ENSG00000214617	4479
+ENSG00000214694	5490
+ENSG00000214810	311
+ENSG00000214961	1372
+ENSG00000214975	499
+ENSG00000215286	754
+ENSG00000215333	1283
+ENSG00000216854	553
+ENSG00000216915	1495
+ENSG00000217716	494
+ENSG00000217801	2171
+ENSG00000218965	609
+ENSG00000219553	723
+ENSG00000220131	354
+ENSG00000220157	961
+ENSG00000220483	871
+ENSG00000221843	6199
+ENSG00000221909	2717
+ENSG00000222046	1869
+ENSG00000223382	1326
+ENSG00000223620	1102
+ENSG00000223877	622
+ENSG00000224016	291
+ENSG00000224520	1447
+ENSG00000224578	1377
+ENSG00000224628	1519
+ENSG00000224664	316
+ENSG00000224892	997
+ENSG00000225405	390
+ENSG00000225544	392
+ENSG00000225787	306
+ENSG00000225806	1521
+ENSG00000226067	2075
+ENSG00000226086	822
+ENSG00000226114	361
+ENSG00000226144	454
+ENSG00000226232	1728
+ENSG00000226268	959
+ENSG00000226478	1126
+ENSG00000226703	812
+ENSG00000226752	7181
+ENSG00000226790	1139
+ENSG00000226833	1438
+ENSG00000227006	861
+ENSG00000227057	3115
+ENSG00000227343	600
+ENSG00000227376	552
+ENSG00000227401	284
+ENSG00000227543	3835
+ENSG00000227666	316
+ENSG00000227742	946
+ENSG00000227968	999
+ENSG00000228118	459
+ENSG00000228195	881
+ENSG00000228236	315
+ENSG00000228599	742
+ENSG00000228612	2737
+ENSG00000228981	843
+ENSG00000229044	439
+ENSG00000229344	682
+ENSG00000229503	477
+ENSG00000229956	6794
+ENSG00000230006	8042
+ENSG00000230022	634
+ENSG00000230074	665
+ENSG00000230118	258
+ENSG00000230146	1176
+ENSG00000230243	319
+ENSG00000230295	351
+ENSG00000230406	421
+ENSG00000230531	1798
+ENSG00000230551	8636
+ENSG00000230650	3130
+ENSG00000230667	909
+ENSG00000230863	742
+ENSG00000230869	2418
+ENSG00000230913	744
+ENSG00000231096	390
+ENSG00000231181	559
+ENSG00000231245	402
+ENSG00000231434	2167
+ENSG00000231615	1337
+ENSG00000231711	4947
+ENSG00000231955	1411
+ENSG00000232186	1228
+ENSG00000232581	357
+ENSG00000232676	1124
+ENSG00000232699	736
+ENSG00000232905	946
+ENSG00000232943	400
+ENSG00000233122	2436
+ENSG00000233454	275
+ENSG00000233503	1501
+ENSG00000233602	619
+ENSG00000233836	3242
+ENSG00000233846	487
+ENSG00000234231	2095
+ENSG00000234639	1239
+ENSG00000234722	3487
+ENSG00000234742	555
+ENSG00000234981	792
+ENSG00000235065	475
+ENSG00000235363	225
+ENSG00000235424	288
+ENSG00000235444	618
+ENSG00000235512	292
+ENSG00000235623	574
+ENSG00000235655	411
+ENSG00000235698	1200
+ENSG00000235750	4783
+ENSG00000235847	965
+ENSG00000235859	1234
+ENSG00000235892	1677
+ENSG00000236086	262
+ENSG00000236285	837
+ENSG00000236290	703
+ENSG00000236330	886
+ENSG00000236468	1335
+ENSG00000236570	1227
+ENSG00000236680	1238
+ENSG00000236681	523
+ENSG00000236735	375
+ENSG00000236739	535
+ENSG00000236753	2715
+ENSG00000236801	474
+ENSG00000236824	13458
+ENSG00000236946	1087
+ENSG00000237017	4158
+ENSG00000237033	609
+ENSG00000237054	3194
+ENSG00000237101	1323
+ENSG00000237357	2579
+ENSG00000237517	7448
+ENSG00000237939	652
+ENSG00000237977	563
+ENSG00000238221	500
+ENSG00000238251	514
+ENSG00000239377	420
+ENSG00000239524	400
+ENSG00000239569	736
+ENSG00000239791	1918
+ENSG00000239887	4495
+ENSG00000239926	747
+ENSG00000240005	589
+ENSG00000240392	575
+ENSG00000240418	893
+ENSG00000240540	1183
+ENSG00000240821	579
+ENSG00000241258	3540
+ENSG00000241370	1606
+ENSG00000241494	438
+ENSG00000241680	375
+ENSG00000241697	2611
+ENSG00000241772	1051
+ENSG00000241923	622
+ENSG00000242061	438
+ENSG00000242140	231
+ENSG00000242349	1427
+ENSG00000242600	2616
+ENSG00000242612	4046
+ENSG00000242858	602
+ENSG00000243122	413
+ENSG00000243396	402
+ENSG00000243701	4206
+ENSG00000243779	321
+ENSG00000244171	1291
+ENSG00000244270	403
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/go_terms.tab	Thu Mar 03 09:56:51 2016 -0500
@@ -0,0 +1,85 @@
+ENSG00000162526	GO:0000003
+ENSG00000162526	GO:0000166
+ENSG00000162526	GO:0000287
+ENSG00000162526	GO:0001882
+ENSG00000162526	GO:0001883
+ENSG00000162526	GO:0003674
+ENSG00000162526	GO:0003824
+ENSG00000162526	GO:0004672
+ENSG00000162526	GO:0004674
+ENSG00000162526	GO:0005488
+ENSG00000162526	GO:0005515
+ENSG00000162526	GO:0005524
+ENSG00000162526	GO:0005575
+ENSG00000162526	GO:0005622
+ENSG00000162526	GO:0005623
+ENSG00000162526	GO:0005737
+ENSG00000162526	GO:0006464
+ENSG00000162526	GO:0006468
+ENSG00000162526	GO:0006793
+ENSG00000162526	GO:0006796
+ENSG00000162526	GO:0007154
+ENSG00000162526	GO:0007165
+ENSG00000162526	GO:0007275
+ENSG00000162526	GO:0007276
+ENSG00000162526	GO:0007283
+ENSG00000162526	GO:0008150
+ENSG00000162526	GO:0008152
+ENSG00000162526	GO:0009987
+ENSG00000162526	GO:0016301
+ENSG00000162526	GO:0016310
+ENSG00000162526	GO:0016740
+ENSG00000162526	GO:0016772
+ENSG00000162526	GO:0016773
+ENSG00000162526	GO:0017076
+ENSG00000162526	GO:0019538
+ENSG00000162526	GO:0019953
+ENSG00000162526	GO:0022414
+ENSG00000162526	GO:0023052
+ENSG00000162526	GO:0030154
+ENSG00000162526	GO:0030554
+ENSG00000162526	GO:0032501
+ENSG00000162526	GO:0032502
+ENSG00000162526	GO:0032504
+ENSG00000162526	GO:0032549
+ENSG00000162526	GO:0032550
+ENSG00000162526	GO:0032553
+ENSG00000162526	GO:0032555
+ENSG00000162526	GO:0032559
+ENSG00000162526	GO:0035556
+ENSG00000162526	GO:0035639
+ENSG00000162526	GO:0036094
+ENSG00000162526	GO:0036211
+ENSG00000162526	GO:0043167
+ENSG00000162526	GO:0043168
+ENSG00000162526	GO:0043169
+ENSG00000162526	GO:0043170
+ENSG00000162526	GO:0043412
+ENSG00000162526	GO:0044237
+ENSG00000162526	GO:0044238
+ENSG00000162526	GO:0044260
+ENSG00000162526	GO:0044267
+ENSG00000162526	GO:0044424
+ENSG00000162526	GO:0044464
+ENSG00000162526	GO:0044699
+ENSG00000162526	GO:0044700
+ENSG00000162526	GO:0044702
+ENSG00000162526	GO:0044703
+ENSG00000162526	GO:0044707
+ENSG00000162526	GO:0044763
+ENSG00000162526	GO:0044767
+ENSG00000162526	GO:0046872
+ENSG00000162526	GO:0048232
+ENSG00000162526	GO:0048609
+ENSG00000162526	GO:0048869
+ENSG00000162526	GO:0050789
+ENSG00000162526	GO:0050794
+ENSG00000162526	GO:0050896
+ENSG00000162526	GO:0051704
+ENSG00000162526	GO:0051716
+ENSG00000162526	GO:0065007
+ENSG00000162526	GO:0071704
+ENSG00000162526	GO:0097159
+ENSG00000162526	GO:0097367
+ENSG00000162526	GO:1901265
+ENSG00000162526	GO:1901363
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in.fasta	Thu Mar 03 09:56:51 2016 -0500
@@ -0,0 +1,2 @@
+>1
+AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAAAAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAATTTTT
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in.gtf	Thu Mar 03 09:56:51 2016 -0500
@@ -0,0 +1,6 @@
+1	ensembl_havana	gene	1	103	.	+	.	gene_id "ENSG00000162526"; gene_version "4"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1";
+1	ensembl_havana	transcript	1	103	.	+	.	gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	exon	1	103	.	+	.	gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; exon_id "ENSE00002319515"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	CDS	1	100	.	+	0	gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; protein_id "ENSP00000334393"; protein_version "3"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	start_codon	1	3	.	+	0	gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	stop_codon	101	103	.	+	0	gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/length.tab	Thu Mar 03 09:56:51 2016 -0500
@@ -0,0 +1,1 @@
+ENSG00000162526	103
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wal.tab	Thu Mar 03 09:56:51 2016 -0500
@@ -0,0 +1,3 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology
+GO:0000278	0.01123506125343	0.999376653834006	4	5	mitotic cell cycle	BP
+GO:0000003	1	0.805913166914891	0	1	reproduction	BP