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changeset 0:ade933eff007 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit b7dcd020c6a15fa55f392cc09cbc37580d6e75c4
author iuc
date Thu, 17 Nov 2016 16:40:19 -0500
parents
children 9d1256d9ef0b
files 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/length.tab test-data/wal.tab
diffstat 9 files changed, 2305 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/goseq.r	Thu Nov 17 16:40:19 2016 -0500
@@ -0,0 +1,121 @@
+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"),
+    make_option(c("-w","--wallenius_tab"), type="character", help="Path to output file with P-values estimated using wallenius distribution."),
+    make_option(c("-s","--sampling_tab"), type="character", default=FALSE, help="Path to output file with P-values estimated using wallenius distribution."),
+    make_option(c("-n","--nobias_tab"), type="character", default=FALSE, help="Path to output file with P-values estimated using wallenius distribution and no correction for gene length bias."),
+    make_option(c("-l","--length_bias_plot"), type="character", default=FALSE, help="Path to length-bias plot."),
+    make_option(c("-sw","--sample_vs_wallenius_plot"), type="character", default=FALSE, help="Path to plot comparing sampling with wallenius p-values."),
+    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("-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("-p", "--p_adj_method"), default="BH", type="character", help="Multiple hypothesis testing correction method to use"),
+    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
+length_file = args$length_file
+genome = args$genome
+gene_id = args$gene_id
+wallenius_tab = args$wallenius_tab
+sampling_tab = args$sampling_tab
+nobias_tab = args$nobias_tab
+length_bias_plot = args$length_bias_plot
+sample_vs_wallenius_plot = args$sample_vs_wallenius_plot
+repcnt = args$repcnt
+p_adj_method = args$p_adj_method
+use_genes_without_cat = args$use_genes_without_cat
+make_plots = args$make_plots
+
+# format DE genes into named vector suitable for goseq
+dge_table = read.delim(dge_file, header = FALSE, sep="\t")
+genes = as.numeric(as.logical(dge_table[,ncol(dge_table)])) # Last column contains TRUE/FALSE
+names(genes) = dge_table[,1] # Assuming first column contains gene names
+
+# gene lengths, assuming last column
+if (length_file != "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),][,ncol(length_table)]
+  } else {
+  gene_lengths = getlength(names(genes), genome, gene_id)
+  }
+
+# Estimate PWF
+
+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 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
+if (wallenius_tab != "" && wallenius_tab!="None") {
+  GO.wall=goseq(pwf, genome = genome, id = gene_id, use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
+  GO.wall$p.adjust.over_represented = p.adjust(GO.wall$over_represented_pvalue, method=p_adj_method)
+  GO.wall$p.adjust.under_represented = p.adjust(GO.wall$under_represented_pvalue, method=p_adj_method)
+  write.table(GO.wall, wallenius_tab, sep="\t", row.names = FALSE, quote = FALSE)
+}
+
+# hypergeometric (no length bias correction)
+if (nobias_tab != "" && nobias_tab != "None") {
+  GO.nobias=goseq(pwf, genome = genome, id = gene_id, method="Hypergeometric", use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
+  GO.nobias$p.adjust.over_represented = p.adjust(GO.nobias$over_represented_pvalue, method=p_adj_method)
+  GO.nobias$p.adjust.under_represented = p.adjust(GO.nobias$under_represented_pvalue, method=p_adj_method)
+  write.table(GO.nobias, nobias_tab, sep="\t", row.names = FALSE, quote = FALSE)
+}
+
+# Sampling distribution
+if (repcnt > 0) {
+  GO.samp=goseq(pwf, genome = genome, id = gene_id, method="Sampling", repcnt=repcnt, use_genes_without_cat = use_genes_without_cat, gene2cat=go_map)
+  GO.samp$p.adjust.over_represented = p.adjust(GO.samp$over_represented_pvalue, method=p_adj_method)
+  GO.samp$p.adjust.under_represented = p.adjust(GO.samp$under_represented_pvalue, method=p_adj_method)
+  write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE)
+  # 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)
+  graphics.off()
+  }
+}
+
+sessionInfo()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/goseq.xml	Thu Nov 17 16:40:19 2016 -0500
@@ -0,0 +1,140 @@
+<tool id="goseq" name="goseq" version="0.2.2">
+    <description>tests for overrepresented gene categories</description>
+    <requirements>
+        <requirement type="package" version="1.3.2">r-optparse</requirement>
+        <requirement type="package" version="1.22.0">bioconductor-goseq</requirement>
+    </requirements>
+    <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>
+    <command><![CDATA[
+        Rscript '$__tool_directory__'/goseq.r --dge_file '$dge_file'
+        --length_file '$length_file'
+        --category_file '$category_file'
+        #if $methods['wallenius']:
+        --wallenius_tab '$wallenius_tab'
+        #end if
+        #if $methods['hypergeometric']:
+        --nobias_tab 'nobias_tab'
+        #end if
+        --repcnt '$methods.repcnt'
+        --sampling_tab '$sampling_tab'
+        --p_adj_method '$p_adj_method'
+        --use_genes_without_cat '$use_genes_without_cat'
+        --make_plots '$make_plots'
+        --length_bias_plot '$length_bias_plot'
+        --sample_vs_wallenius_plot '$sample_vs_wallenius_plot'
+    ]]></command>
+    <inputs>
+        <param name="dge_file" help="A tabular file with gene names in the first column, and TRUE or FALSE in the last column. TRUE means a gene is differentially expressed. See help section for details." label="Differentially expressed gene file" type="data" format="tabular" />
+        <param name="length_file" label="Gene length file for length bias correction" help="You can calculate the gene length using the get length and gc content tool" type="data" format="tabular" />
+        <param name="category_file" label="Gene category file" help="You can obtain a mapping of gene id to gene ontology using the getgo tool" type="data" format="tabular" />
+        <param name="use_genes_without_cat" 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"
+               label="Count genes without any category?" type="boolean"/>
+        <section name="methods" title="Method options" expanded="True">
+            <param name="wallenius" type="boolean" checked="true" label="Use wallenius method" help="See help for details" />
+            <param name="hypergeometric" type="boolean" checked="false" label="Use hypergeometric method" help="Does not use gene length information. See help for details" />
+            <param name="repcnt" help="Draw this many random control gene sets. Set to 0 to not do sampling. Larger values take a long time" label="sampling depth" size="3" type="integer" min="0" max="10000" value="0" />
+        </section>
+        <param name="p_adj_method" type="select" label="Select a method for multiple hypothesis testing correction">
+            <option value="BH" selected="true">Benjamini-Hochberg [FDR] (1995)</option>
+            <option value="holm">Holm (1979)</option>
+            <option value="hommel">Hommel (1988)</option>
+            <option value="hochberg">Hochberg (1988)</option>
+            <option value="bonferroni">Bonferroni</option>
+            <option value="BY">Benjamini - Yekutieli (2001)</option>
+        </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>
+    </inputs>
+    <outputs>
+        <data name="length_bias_plot" format="pdf" label="length bias plot">
+            <filter>make_plots</filter>
+            <filter>methods['hypergeometric']</filter>
+        </data>
+        <data name="sample_vs_wallenius_plot" format="pdf" label="Plot P-value from sampling against wallenius distribution">
+            <filter>methods['repcnt'] != 0</filter>
+            <filter>methods['wallenius']</filter>
+            <filter>make_plots</filter>
+        </data>
+        <data name="nobias_tab" format="tabular" label="Ranked category list - no length bias correction">
+            <filter>methods['hypergeometric']</filter>
+        </data>
+        <data name="sampling_tab" format="tabular" label="Ranked category list - sampling">
+            <filter>methods['repcnt'] != 0</filter>
+        </data>
+        <data name="wallenius_tab" format="tabular" label="Ranked category list - wallenius method">
+            <filter>methods['wallenius']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="dge_file" value="dge_list.tab" ftype="tabular"/>
+            <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" />
+            <output name="wallenius_tab" file="wal.tab" compare="re_match"/>
+        </test>
+    </tests>
+    <help>
+
+        **What it does**
+
+        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**
+
+        *DGE list:*
+        goseq needs a tabular file with genes in the first column, and TRUE or FALSE in the last column.
+        TRUE means the gene should count as differentially expressed, FALSE means it is not differentially expressed.
+        You can use the "Compute an expression on every row" tool to create a TRUE / FALSE column for your dataset.
+
+        *Gene length file:*
+        goseq needs information about the length of a gene to correct for potential length bias in differentially expressed genes
+        using a prodbability weight function (PWF).
+        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.
+
+        *Gene category 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.
+
+        **Method options**
+
+        3 methods, "Wallenius", "Sampling" and "Hypergeometric", can be used to calculate the p-values as follows.
+
+        *"Wallenius"* approximates the true distribution of numbers of members of a category amongst DE genes by the Wallenius non-central hypergeometric distribution.
+        This distribution assumes that within a category all genes have the same probability of being chosen.
+        Therefore, this approximation works best when the range in probabilities obtained by the probability weighting function is small.
+
+        *"Sampling"* uses random sampling to approximate the true distribution and uses it to calculate the p-values for over (and under) representation of categories.
+        Although this is the most accurate method given a high enough value of sampling depth, its use quickly becomes computationally prohibitive.
+
+        *"Hypergeometric"* assumes there is no bias in power to detect differential expression at all and calculates the p-values using a standard hypergeometric distribution.
+        Useful if you wish to test the effect of selection bias on your results.
+
+        CAUTION:  "Hypergeometric" should NEVER be used for producing results for biological interpretation.
+        If there is genuinely no bias in power to detect DE in your experiment, the PWF will reflect this and the other methods will produce accuracte results.
+
+        .. _manual: https://bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf
+
+
+    </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/test-data/category.tab	Thu Nov 17 16:40:19 2016 -0500
@@ -0,0 +1,6 @@
+ENSG00000162526	GO:0000003
+ENSG00000198648	GO:0000278
+ENSG00000112312	GO:0000278
+ENSG00000174442	GO:0000278
+ENSG00000108953	GO:0000278
+ENSG00000167842	GO:0000278
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dge_list.tab	Thu Nov 17 16:40:19 2016 -0500
@@ -0,0 +1,1000 @@
+ENSG00000140459	False
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gc.tab	Thu Nov 17 16:40:19 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 Nov 17 16:40:19 2016 -0500
@@ -0,0 +1,948 @@
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+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 Nov 17 16:40:19 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/length.tab	Thu Nov 17 16:40:19 2016 -0500
@@ -0,0 +1,1 @@
+ENSG00000162526	103
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/wal.tab	Thu Nov 17 16:40:19 2016 -0500
@@ -0,0 +1,3 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	p\.adjust.over_represented	p\.adjust.under_represented
+GO:0000278	0\.0122.+	0\.999.+	4	5	mitotic cell cycle	BP	0\.0245.+	0\.999.+
+GO:0000003	1	0\.796.+	0	1	reproduction	BP	1	0\.999.+