Repository 'deseq2'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/deseq2

Changeset 19:c56e0689e46e (2018-12-04)
Previous changeset 18:3bf1b3ec1ddf (2018-11-16) Next changeset 20:89d26b11d452 (2018-12-06)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
modified:
deseq2.R
deseq2.xml
get_deseq_dataset.R
test-data/tx2gene.tab
added:
test-data/GRCh38_latest_genomic.gff
b
diff -r 3bf1b3ec1ddf -r c56e0689e46e deseq2.R
--- a/deseq2.R Fri Nov 16 14:47:19 2018 -0500
+++ b/deseq2.R Tue Dec 04 08:19:06 2018 -0500
b
@@ -57,7 +57,7 @@
   "plots" , "p", 1, "character",
   "tximport", "i", 0, "logical",
   "txtype", "y", 1, "character",
-  "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF)
+  "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF/GFF3 file
   "esf", "e", 1, "character",
   "fit_type", "t", 1, "integer",
   "many_contrasts", "m", 0, "logical",
b
diff -r 3bf1b3ec1ddf -r c56e0689e46e deseq2.xml
--- a/deseq2.xml Fri Nov 16 14:47:19 2018 -0500
+++ b/deseq2.xml Tue Dec 04 08:19:06 2018 -0500
[
b'@@ -1,11 +1,16 @@\n-<tool id="deseq2" name="DESeq2" version="2.11.40.3">\n+<tool id="deseq2" name="DESeq2" version="2.11.40.4">\n     <description>Determines differentially expressed features from count tables</description>\n     <requirements>\n-        <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>\n-        <requirement type="package" version="1.6.0">bioconductor-tximport</requirement>\n-        <requirement type="package" version="1.30.0">bioconductor-genomicfeatures</requirement>\n-        <requirement type="package" version="0.6.5">r-ggrepel</requirement>\n-        <requirement type="package" version="1.0.8">r-pheatmap</requirement>\n+        <requirement type="package" version="1.20.0">bioconductor-deseq2</requirement>\n+        <!-- Optional dependency of tximport, needed to import kallisto results https://github.com/galaxyproject/usegalaxy-playbook/issues/161 -->\n+        <requirement type="package" version="2.24.0">bioconductor-rhdf5</requirement>\n+        <requirement type="package" version="1.8.0">bioconductor-tximport</requirement>\n+        <requirement type="package" version="1.32.3">bioconductor-genomicfeatures</requirement>\n+        <requirement type="package" version="1.20.2">r-getopt</requirement>\n+        <requirement type="package" version="0.8.0">r-ggrepel</requirement>\n+        <requirement type="package" version="3.0.1">r-gplots</requirement>\n+        <requirement type="package" version="1.0.10">r-pheatmap</requirement>\n+        <requirement type="package" version="0.2.20">r-rjson</requirement>\n     </requirements>\n     <stdio>\n         <regex match="Execution halted"\n@@ -27,7 +32,7 @@\n     <command><![CDATA[\n #if $tximport.tximport_selector == \'tximport\':\n     #if $tximport.mapping_format.mapping_format_selector == \'gtf\':\n-        ln -s \'$tximport.mapping_format.gtf_file\' mapping.gtf &&\n+        ln -s \'$tximport.mapping_format.gtf_file\' mapping.gff &&\n     #else:\n         ln -s \'$tximport.mapping_format.tabular_file\' mapping.txt &&\n     #end if\n@@ -92,7 +97,7 @@\n         -i\n         -y $tximport.txtype\n         #if $tximport.mapping_format.mapping_format_selector == \'gtf\':\n-            -x mapping.gtf\n+            -x mapping.gff\n         #else:\n             -x mapping.txt\n         #end if\n@@ -133,14 +138,14 @@\n                 </param>\n                 <conditional name="mapping_format">\n                     <param name="mapping_format_selector" type="select" label="Gene mapping format">\n-                        <option value="gtf" selected="True">GTF</option>\n-                        <option value="tabular">Transcript-ID and Gene-ID mapping file</option>\n+                        <option value="gtf" selected="True">GTF/GFF3</option>\n+                        <option value="tabular">Transcript-ID to Gene-ID mapping file</option>\n                     </param>\n                     <when value="gtf">\n-                        <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 file with Transcript - Gene mapping"/>\n+                        <param name="gtf_file" type="data" format="gtf,gff3" label="GTF/GFF3 annotation file"/>\n                     </when>\n                     <when value="tabular">\n-                        <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript - Gene mapping"/>\n+                        <param name="tabular_file" type="data" format="tabular" label="Tabular file with Transcript-ID to Gene-ID mapping"/>\n                     </when>\n                 </conditional>\n             </when>\n@@ -190,7 +195,7 @@\n             help=" DESeq2 performs independent \xef\xac\x81ltering by default using the mean of normalized counts as a \xef\xac\x81lter statistic" />\n     </inputs>\n     <outputs>\n-        <data format="tabular" name="deseq_out" label="DESeq2 result file on ${on_string}">\n+        <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}">\n             <filter>many_contrasts is False</filter>\n       '..b'ny_contrasts is True</filter>\n             <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>\n         </collection>\n-        <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">\n+        <data name="plots" format="pdf" label="DESeq2 plots on ${on_string}">\n             <filter>pdf == True</filter>\n         </data>\n-        <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}">\n+        <data name="counts_out" format="tabular" label="Normalized counts file on ${on_string}">\n             <filter>normCounts == True</filter>\n         </data>\n-        <data format="tabular" name="rlog_out" label="rLog-Normalized counts file on ${on_string}">\n+        <data name="rlog_out" format="tabular" label="rLog-Normalized counts file on ${on_string}">\n             <filter>normRLog == True</filter>\n         </data>\n-        <data format="tabular" name="vst_out" label="VST-Normalized counts file on ${on_string}">\n+        <data name="vst_out" format="tabular" label="VST-Normalized counts file on ${on_string}">\n             <filter>normVST == True</filter>\n         </data>\n     </outputs>\n@@ -251,7 +256,7 @@\n             </output>\n             <output name="deseq_out" >\n                 <assert_contents>\n-                    <has_text_matching expression="FBgn0003360\\t1933.9504.*\\t-2.8399.*\\t0.1309.*-21.6851.*2.831.*8.024" />\n+                    <has_text_matching expression="FBgn0003360\\t1933\\.9504.*\\t-2\\.8399.*\\t0\\.1309.*\\t-21\\.68.*\\t.*e-104\\t.*e-101" />\n                 </assert_contents>\n             </output>\n         </test>\n@@ -315,7 +320,7 @@\n             </output>\n             <output name="deseq_out" >\n                 <assert_contents>\n-                    <has_text_matching expression="FBgn0003360\\t1933.9504.*\\t-2.8399.*\\t0.1309.*-21.6851.*2.831.*8.024" />\n+                    <has_text_matching expression="FBgn0003360\\t1933\\.9504.*\\t-2\\.8399.*\\t0\\.1309.*\\t-21\\.68.*\\t.*e-104\\t.*e-101" />\n                 </assert_contents>\n             </output>\n         </test>\n@@ -339,7 +344,31 @@\n             <param name="tabular_file" value="tx2gene.tab"/>\n             <output name="deseq_out" >\n                 <assert_contents>\n-                    <has_text_matching expression="MIR6859-2\\t1.1858.*\\t-1.5832.*\\t1.2956.*\\t-1.2219.*\\t0.2217.*\\t0.8868.*" />\n+                    <has_text_matching expression="UGT3A2\\t1.8841.*\\t-0.1329.*\\t0.6936.*\\t-0.1917.*\\t0.8479.*\\t0.9999.*" />\n+                </assert_contents>\n+            </output>\n+        </test>\n+        <!--Ensure Sailfish/Salmon input with GFF3 annotation works-->\n+        <test expect_num_outputs="1">\n+            <repeat name="rep_factorName">\n+                <param name="factorName" value="Treatment"/>\n+                <repeat name="rep_factorLevel">\n+                    <param name="factorLevel" value="Treated"/>\n+                    <param name="countsFile" value="sailfish/sailfish_quant.sf1.tab,sailfish/sailfish_quant.sf2.tab,sailfish/sailfish_quant.sf3.tab"/>\n+                </repeat>\n+                <repeat name="rep_factorLevel">\n+                    <param name="factorLevel" value="Untreated"/>\n+                    <param name="countsFile" value="sailfish/sailfish_quant.sf4.tab,sailfish/sailfish_quant.sf5.tab,sailfish/sailfish_quant.sf6.tab"/>\n+                </repeat>\n+            </repeat>\n+            <param name="pdf" value="False"/>\n+            <param name="tximport_selector" value="tximport"/>\n+            <param name="txtype" value="sailfish"/>\n+            <param name="mapping_format_selector" value="gtf"/>\n+            <param name="gtf_file" value="GRCh38_latest_genomic.gff"/>\n+            <output name="deseq_out" >\n+                <assert_contents>\n+                    <has_text_matching expression="UGT3A2\\t1.8841.*\\t-0.1329.*\\t0.6936.*\\t-0.1917.*\\t0.8479.*\\t0.9999.*" />\n                 </assert_contents>\n             </output>\n         </test>\n'
b
diff -r 3bf1b3ec1ddf -r c56e0689e46e get_deseq_dataset.R
--- a/get_deseq_dataset.R Fri Nov 16 14:47:19 2018 -0500
+++ b/get_deseq_dataset.R Tue Dec 04 08:19:06 2018 -0500
[
@@ -9,11 +9,11 @@
   }
 
   if (!is.null(tximport)) {
-    if (is.null(tx2gene)) stop("A transcript-to-gene map or a GTF file is required for tximport")
-    if (tolower(file_ext(opt$tx2gene)) == "gtf") {
-      gtfFile <-tx2gene
+    if (is.null(tx2gene)) stop("A transcript-to-gene map or a GTF/GFF3 file is required for tximport")
+    if (tolower(file_ext(opt$tx2gene)) == "gff") {
+      gffFile <-tx2gene
     } else {
-      gtfFile <- NULL
+      gffFile <- NULL
       tx2gene <- read.table(tx2gene, header=FALSE)
     }
     useTXI <- TRUE
@@ -45,22 +45,26 @@
 
   } else {
       # construct the object using tximport
-      # first need to make the tx2gene table
-      # this takes ~2-3 minutes using Bioconductor functions
-      if (!is.null(gtfFile)) {
-        suppressPackageStartupMessages({
-          library("GenomicFeatures")
-        })
-        txdb <- makeTxDbFromGFF(gtfFile, format="gtf")
-        k <- keys(txdb, keytype = "GENEID")
-        df <- select(txdb, keys = k, keytype = "GENEID", columns = "TXNAME")
-        tx2gene <- df[, 2:1]  # tx ID, then gene ID
-      }
       library("tximport")
       txiFiles <- as.character(sampleTable$filename)
       labs <- row.names(sampleTable)
       names(txiFiles) <- labs
-      txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene)
+      if (!is.null(gffFile)) {
+        # first need to make the tx2gene table
+        # this takes ~2-3 minutes using Bioconductor functions
+        suppressPackageStartupMessages({
+          library("GenomicFeatures")
+        })
+        txdb <- makeTxDbFromGFF(gffFile)
+        k <- keys(txdb, keytype = "TXNAME")
+        tx2gene <- select(txdb, k, "GENEID", "TXNAME")
+      }
+      try(txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene))
+      if (!exists("txi")) {
+        # Remove version from transcript IDs
+        tx2gene$TXNAME <- sub('\\.[0-9]+', '', tx2gene$TXNAME)
+        txi <- tximport(txiFiles, type=txtype, tx2gene=tx2gene)
+      }
       dds <- DESeqDataSetFromTximport(txi,
                                       subset(sampleTable, select=-c(filename)),
                                       designFormula)
b
diff -r 3bf1b3ec1ddf -r c56e0689e46e test-data/GRCh38_latest_genomic.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GRCh38_latest_genomic.gff Tue Dec 04 08:19:06 2018 -0500
b
b'@@ -0,0 +1,86 @@\n+##gff-version 3\n+#!gff-spec-version 1.21\n+#!processor NCBI annotwriter\n+#!genome-build GRCh38.p12\n+#!genome-build-accession NCBI_Assembly:GCF_000001405.38\n+#!annotation-source NCBI Homo sapiens Annotation Release 109\n+# Trimmed version of ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz\n+##sequence-region NC_000005.10 1 181538259\n+##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606\n+NC_000005.10\tRefSeq\tregion\t1\t181538259\t.\t+\t.\tID=id565344;Dbxref=taxon:9606;Name=5;chromosome=5;gbkey=Src;genome=chromosome;mol_type=genomic DNA\n+NC_000005.10\tBestRefSeq%2CGnomon\tgene\t36035017\t36071358\t.\t-\t.\tID=gene14857;Dbxref=GeneID:167127,HGNC:HGNC:27266,MIM:616384;Name=UGT3A2;description=UDP glycosyltransferase family 3 member A2;gbkey=Gene;gene=UGT3A2;gene_biotype=protein_coding\n+NC_000005.10\tBestRefSeq\tmRNA\t36035017\t36066921\t.\t-\t.\tID=rna45581;Parent=gene14857;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;Name=NM_001168316.1;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1\n+NC_000005.10\tBestRefSeq\texon\t36066696\t36066921\t.\t-\t.\tID=id576076;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1\n+NC_000005.10\tBestRefSeq\texon\t36051870\t36051984\t.\t-\t.\tID=id576077;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1\n+NC_000005.10\tBestRefSeq\texon\t36048889\t36049420\t.\t-\t.\tID=id576078;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1\n+NC_000005.10\tBestRefSeq\texon\t36039477\t36039708\t.\t-\t.\tID=id576079;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1\n+NC_000005.10\tBestRefSeq\texon\t36037797\t36038016\t.\t-\t.\tID=id576080;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1\n+NC_000005.10\tBestRefSeq\texon\t36035017\t36035974\t.\t-\t.\tID=id576081;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1\n+NC_000005.10\tBestRefSeq\ttranscript\t36035017\t36066921\t.\t-\t.\tID=rna45582;Parent=gene14857;Dbxref=GeneID:167127,Genbank:NR_031764.1,HGNC:HGNC:27266,MIM:616384;Name=NR_031764.1;gbkey=misc_RNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 3;transcript_id=NR_031764.1\n+NC_000005.10\tBestRefSeq\texon\t36066696\t36066921\t.\t-\t.\tID=id576082;Parent=rna45582;Dbxref=GeneID:167127,Genbank:NR_031764.1,HGNC:HGNC:27266,MIM:616384;gbkey=misc_RNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 3;transcript_id=NR_031764.1\n+NC_000005.10\tBestRefSeq\texon\t36064249\t36064350\t.\t-\t.\tID=id576083;Parent=rna45582;Dbxref=GeneID:167127,Genbank:NR_031764.1,HGNC:HGNC:27266,MIM:616384;gbkey=misc_RNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 3;transcript_id=NR_031764.1\n+NC_000005.10\tBestRefSeq\texon\t36051870\t36051984\t.\t-\t.\tID=id576084;Parent=rna45582;Dbxref=GeneID:167127,Genbank:NR_031764.1,HGNC:HGNC:27266,MIM:616384;gbkey=misc_RNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 3;transcript_id=NR_031764.1\n+'..b'isc_RNA;gene=HOXC5;product=homeobox C5%2C transcript variant 2;transcript_id=NR_003084.2\n+NC_000012.12\tBestRefSeq\texon\t54034278\t54035361\t.\t+\t.\tID=id1209167;Parent=rna100349;Dbxref=GeneID:3222,Genbank:NR_003084.2,HGNC:HGNC:5127,MIM:142973;gbkey=misc_RNA;gene=HOXC5;product=homeobox C5%2C transcript variant 2;transcript_id=NR_003084.2\n+NC_000012.12\tBestRefSeq\tmRNA\t54033048\t54035361\t.\t+\t.\tID=rna100350;Parent=gene33487;Dbxref=GeneID:3222,Genbank:NM_018953.3,HGNC:HGNC:5127,MIM:142973;Name=NM_018953.3;gbkey=mRNA;gene=HOXC5;product=homeobox C5%2C transcript variant 1;transcript_id=NM_018953.3\n+NC_000012.12\tBestRefSeq\texon\t54033048\t54033576\t.\t+\t.\tID=id1209168;Parent=rna100350;Dbxref=GeneID:3222,Genbank:NM_018953.3,HGNC:HGNC:5127,MIM:142973;gbkey=mRNA;gene=HOXC5;product=homeobox C5%2C transcript variant 1;transcript_id=NM_018953.3\n+NC_000012.12\tBestRefSeq\texon\t54034278\t54035361\t.\t+\t.\tID=id1209169;Parent=rna100350;Dbxref=GeneID:3222,Genbank:NM_018953.3,HGNC:HGNC:5127,MIM:142973;gbkey=mRNA;gene=HOXC5;product=homeobox C5%2C transcript variant 1;transcript_id=NM_018953.3\n+NC_000012.12\tBestRefSeq\tgene\t54016852\t54030823\t.\t+\t.\tID=gene33488;Dbxref=GeneID:3223,HGNC:HGNC:5128,MIM:142972;Name=HOXC6;description=homeobox C6;gbkey=Gene;gene=HOXC6;gene_biotype=protein_coding;gene_synonym=CP25,HHO.C8,HOX3,HOX3C\n+NC_000012.12\tBestRefSeq\tmRNA\t54016852\t54030823\t.\t+\t.\tID=rna100351;Parent=gene33488;Dbxref=GeneID:3223,Genbank:NM_153693.4,HGNC:HGNC:5128,MIM:142972;Name=NM_153693.4;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 2;transcript_id=NM_153693.4\n+NC_000012.12\tBestRefSeq\texon\t54016852\t54017414\t.\t+\t.\tID=id1209172;Parent=rna100351;Dbxref=GeneID:3223,Genbank:NM_153693.4,HGNC:HGNC:5128,MIM:142972;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 2;transcript_id=NM_153693.4\n+NC_000012.12\tBestRefSeq\texon\t54028576\t54028921\t.\t+\t.\tID=id1209173;Parent=rna100351;Dbxref=GeneID:3223,Genbank:NM_153693.4,HGNC:HGNC:5128,MIM:142972;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 2;transcript_id=NM_153693.4\n+NC_000012.12\tBestRefSeq\texon\t54029655\t54030823\t.\t+\t.\tID=id1209174;Parent=rna100351;Dbxref=GeneID:3223,Genbank:NM_153693.4,HGNC:HGNC:5128,MIM:142972;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 2;transcript_id=NM_153693.4\n+NC_000012.12\tBestRefSeq\tmRNA\t54028410\t54030823\t.\t+\t.\tID=rna100352;Parent=gene33488;Dbxref=GeneID:3223,Genbank:NM_004503.3,HGNC:HGNC:5128,MIM:142972;Name=NM_004503.3;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 1;transcript_id=NM_004503.3\n+NC_000012.12\tBestRefSeq\texon\t54028410\t54028921\t.\t+\t.\tID=id1209175;Parent=rna100352;Dbxref=GeneID:3223,Genbank:NM_004503.3,HGNC:HGNC:5128,MIM:142972;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 1;transcript_id=NM_004503.3\n+NC_000012.12\tBestRefSeq\texon\t54029655\t54030823\t.\t+\t.\tID=id1209176;Parent=rna100352;Dbxref=GeneID:3223,Genbank:NM_004503.3,HGNC:HGNC:5128,MIM:142972;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 1;transcript_id=NM_004503.3\n+NC_000012.12\tRefSeq\tcDNA_match\t53973126\t53973923\t798\t+\t.\tID=46c4f9c5-f2cf-415e-a892-fbd053a8f7eb;Target=NM_014212.3 1 798 +;assembly_bases_aln=152;assembly_bases_seq=152;consensus_splices=2;exon_identity=0.991241;for_remapping=2;gap_count=1;identity=0.991241;idty=1;matches=2037;num_ident=2037;num_mismatch=0;pct_coverage=99.1241;pct_coverage_hiqual=99.1241;pct_identity_gap=99.1241;pct_identity_ungap=100;product_coverage=1;rank=1;splices=2;weighted_identity=0.991461\n+NC_000012.12\tRefSeq\tcDNA_match\t53975181\t53976419\t1232.82\t+\t.\tID=46c4f9c5-f2cf-415e-a892-fbd053a8f7eb;Target=NM_014212.3 799 2055 +;assembly_bases_aln=152;assembly_bases_seq=152;consensus_splices=2;exon_identity=0.991241;for_remapping=2;gap_count=1;identity=0.991241;idty=0.98568;matches=2037;num_ident=2037;num_mismatch=0;pct_coverage=99.1241;pct_coverage_hiqual=99.1241;pct_identity_gap=99.1241;pct_identity_ungap=100;product_coverage=1;rank=1;splices=2;weighted_identity=0.991461;Gap=M705 I18 M534\n'
b
diff -r 3bf1b3ec1ddf -r c56e0689e46e test-data/tx2gene.tab
--- a/test-data/tx2gene.tab Fri Nov 16 14:47:19 2018 -0500
+++ b/test-data/tx2gene.tab Tue Dec 04 08:19:06 2018 -0500
b
@@ -1,16 +1,16 @@
 TXNAME GENEID
-NM_001168316 DDX11L1
-NM_174914 DDX11L1
-NR_031764 DDX11L1
-NM_004503 WASH7P
-NM_006897 WASH7P
-NM_014212 WASH7P
-NM_014620 WASH7P
-NM_017409 WASH7P
-NM_017410 WASH7P
-NM_018953 MIR6859-2
-NM_022658 MIR6859-1
-NM_153633 WASH7P
-NM_153693 WASH7P
-NM_173860 WASH7P
-NR_003084 WASH7P
+NM_001168316 UGT3A2
+NM_174914 UGT3A2
+NR_031764 UGT3A2
+NM_004503 HOXC6
+NM_006897 HOXC9
+NM_014212 HOXC11
+NM_014620 HOXC4
+NM_017409 HOXC10
+NM_017410 HOXC13
+NM_018953 HOXC5
+NM_022658 HOXC8
+NM_153633 HOXC4
+NM_153693 HOXC6
+NM_173860 HOXC12
+NR_003084 HOXC5