| Previous changeset 1:f1c406f9554c (2017-01-29) Next changeset 3:f89c9b25feb4 (2018-07-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c |
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modified:
dexseq.R dexseq.xml dexseq_count.xml test-data/dexseq_result.tabular test-data/flattened.gtf |
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added:
macros.xml test-data/dexseq_result_2fact.tabular |
| b |
| diff -r f1c406f9554c -r 6e8b61c54ff3 dexseq.R --- a/dexseq.R Sun Jan 29 06:59:35 2017 -0500 +++ b/dexseq.R Sun Jan 28 04:04:39 2018 -0500 |
| b |
| @@ -3,9 +3,11 @@ # we need that to not crash galaxy with an UTF8 error on German LC settings. Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") -library("DEXSeq") -library('getopt') -library('rjson') +suppressPackageStartupMessages({ + library("DEXSeq") + library('getopt') + library('rjson') +}) options(stringAsfactors = FALSE, useFancyQuotes = FALSE) @@ -90,7 +92,7 @@ BPPARAM=MulticoreParam(workers=opt$threads) dxd <- estimateDispersions(dxd, formula=formulaFullModel, BPPARAM=BPPARAM) print("Estimated dispersions") -dxd <- testForDEU(dxd, fullModel=formulaFullModel, BPPARAM=BPPARAM) +dxd <- testForDEU(dxd, reducedModel=formulaReducedModel, fullModel=formulaFullModel, BPPARAM=BPPARAM) print("tested for DEU") dxd <- estimateExonFoldChanges(dxd, fitExpToVar=primaryFactor, BPPARAM=BPPARAM) print("Estimated fold changes") @@ -111,7 +113,7 @@ if ( !is.null(opt$reportdir) ) { save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData")) save.image() - DEXSeqHTML(res, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA")) + DEXSeqHTML(res, fitExpToVar=primaryFactor, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA")) unlink(file.path(opt$reportdir,"DEXSeq_analysis.RData")) } sessionInfo() |
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| diff -r f1c406f9554c -r 6e8b61c54ff3 dexseq.xml --- a/dexseq.xml Sun Jan 29 06:59:35 2017 -0500 +++ b/dexseq.xml Sun Jan 28 04:04:39 2018 -0500 |
| [ |
| @@ -1,10 +1,12 @@ -<tool id="dexseq" name="DEXSeq" version="1.20.1"> +<tool id="dexseq" name="DEXSeq" version="@VERSION@.0"> <description>Determines differential exon usage from count tables</description> - <requirements> - <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> <requirement type="package" version="1.20.0">r-getopt</requirement> <requirement type="package" version="0.2.15">r-rjson</requirement> - </requirements> + </expand> <code file="dexseq_helper.py" /> <stdio> <regex match="Execution halted" @@ -24,50 +26,45 @@ level="fatal" description="Error in the R script." /> </stdio> - <version_command> - <![CDATA[ - echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")" - ]]> - </version_command> - <command> - <![CDATA[ - mkdir ./html_out && - #import json - Rscript '$__tool_directory__/dexseq.R' - -o '$dexseq_out' - -p \${GALAXY_SLOTS:-4} - #set $temp_factor_names = list() - #for $factor in $rep_factorName: - #set $temp_factor = list() - #set $count_files1 = list() - #for $file in $factor.countFiles1: - $count_files1.append(str($file)) - #end for - $temp_factor.append( {str($factor.factorLevel1): $count_files1} ) + <version_command><![CDATA[ +echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")" + ]]></version_command> + <command><![CDATA[ + mkdir ./html_out && + #import json + Rscript '$__tool_directory__/dexseq.R' + -o '$dexseq_out' + -p \${GALAXY_SLOTS:-4} + #set $temp_factor_names = list() + #for $factor in $rep_factorName: + #set $temp_factor = list() + #set $count_files1 = list() + #for $file in $factor.countFiles1: + $count_files1.append(str($file)) + #end for + $temp_factor.append( {str($factor.factorLevel1): $count_files1} ) - #set $count_files2 = list() - #for $file in $factor.countFiles2: - $count_files2.append(str($file)) - #end for - $temp_factor.append( {str($factor.factorLevel2): $count_files2} ) - $temp_factor_names.append([str($factor.factorName), $temp_factor]) - #end for - -f '#echo json.dumps(temp_factor_names)#' - -a $gtf - -c $fdr_cutoff + #set $count_files2 = list() + #for $file in $factor.countFiles2: + $count_files2.append(str($file)) + #end for + $temp_factor.append( {str($factor.factorLevel2): $count_files2} ) + $temp_factor_names.append([str($factor.factorName), $temp_factor]) + #end for + -f '#echo json.dumps(temp_factor_names)#' + -a $gtf + -c $fdr_cutoff - #if $report: - -r ./html_out - && - mkdir '$htmlreport.extra_files_path' - && - cp ./html_out/testForDEU.html $htmlreport - && - cp -r ./html_out/* '$htmlreport.extra_files_path' - #end if - - ]]> - </command> + #if $report: + -r ./html_out + && + mkdir '$htmlreport.extra_files_path' + && + cp ./html_out/testForDEU.html $htmlreport + && + cp -r ./html_out/* '$htmlreport.extra_files_path' + #end if + ]]></command> <inputs> <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/> <repeat name="rep_factorName" title="Factor" min="1"> @@ -105,7 +102,36 @@ </data> </outputs> <tests> - <test> + <!-- Ensure default output works--> + <test expect_num_outputs="1"> + <param name="gtf" value="dexseq.gtf" ftype="gtf"/> + <repeat name="rep_factorName"> + <param name="factorName" value="condition"/> + <param name="factorLevel1" value="knockdown"/> + <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/> + <param name="factorLevel2" value="control"/> + <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/> + </repeat> + <param name="report" value="False"/> + <param name="fdr_cutoff" value="1"/> + <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/> + </test> + <!-- Ensure report works--> + <test expect_num_outputs="2"> + <param name="gtf" value="dexseq.gtf" ftype="gtf"/> + <repeat name="rep_factorName"> + <param name="factorName" value="Treatment"/> + <param name="factorLevel1" value="knockdown"/> + <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/> + <param name="factorLevel2" value="control"/> + <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/> + </repeat> + <param name="report" value="True"/> + <param name="fdr_cutoff" value="1"/> + <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/> + </test> + <!-- Ensure two factors works--> + <test expect_num_outputs="1"> <param name="gtf" value="dexseq.gtf" ftype="gtf"/> <repeat name="rep_factorName"> <param name="factorName" value="condition"/> @@ -123,11 +149,10 @@ </repeat> <param name="report" value="False"/> <param name="fdr_cutoff" value="0.05"/> - <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/> + <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular"/> </test> </tests> - <help> - <![CDATA[ + <help><![CDATA[ .. class:: infomark **What it does** @@ -139,7 +164,7 @@ DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually. DEXSeq_ is capable of handling multiple factors that effect your experiment. The first factor you input is considered as the primary -factor that affects gene expressions. Primary factor should always be named as 'condition'. You also input several secondary factors that might +factor that affects gene expressions. You also input several secondary factors that might influence your experiment. But the final output will be changes in genes due to primary factor in presence of secondary factors. Each factor has two levels/states. You need to select appropriate count table from your history for each factor level. @@ -186,8 +211,7 @@ .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html - ]]> - </help> + ]]></help> <citations> <citation type="doi">10.1101/gr.133744.111</citation> </citations> |
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| diff -r f1c406f9554c -r 6e8b61c54ff3 dexseq_count.xml --- a/dexseq_count.xml Sun Jan 29 06:59:35 2017 -0500 +++ b/dexseq_count.xml Sun Jan 28 04:04:39 2018 -0500 |
| [ |
| @@ -1,9 +1,11 @@ -<tool id="dexseq_count" name="DEXSeq-Count" version="1.20.1"> +<tool id="dexseq_count" name="DEXSeq-Count" version="@VERSION@.0"> <description>Prepare and count exon abundancies from RNA-seq data</description> - <requirements> - <requirement type="package" version="1.20.1">bioconductor-dexseq</requirement> - <requirement type="package" version="0.6.1.post1">htseq</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="0.9.1">htseq</requirement> + </expand> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" /> @@ -12,26 +14,24 @@ <regex match="Error:" /> <regex match="Exception:" /> </stdio> - <command> - <![CDATA[ - #if $mode.mode_select == "prepare": - dexseq_prepare_annotation.py - -r $mode.aggregate - '$mode.gtffile' - '$flattened_gtf_out' - #elif $mode.mode_select == "count": - dexseq_count.py - -f bam - -p $mode.paired - -s $mode.stranded - -a $mode.qual - -r $mode.order - $mode.flattened_gtf_in - '$mode.bamfile' - '$counts_file' - #end if - ]]> - </command> + <command><![CDATA[ +#if $mode.mode_select == "prepare": + dexseq_prepare_annotation.py + -r $mode.aggregate + '$mode.gtffile' + '$flattened_gtf_out' +#elif $mode.mode_select == "count": + dexseq_count.py + -f bam + -p $mode.paired + -s $mode.stranded + -a $mode.qual + -r $mode.order + $mode.flattened_gtf_in + '$mode.bamfile' + '$counts_file' +#end if + ]]></command> <inputs> <conditional name="mode"> <param name="mode_select" type="select" label="Mode of operation"> @@ -76,33 +76,31 @@ <param name="mode_select" value="prepare" /> <param name="gtffile" ftype="gff" value="original.gtf"/> <param name="aggregate" value="True"/> - <output name="flattened_gtf_out" file="flattened.gtf" ftype="gtf"/> + <output name="flattened_gtf_out" ftype="gtf" compare="sim_size" file="flattened.gtf"/> </test> </tests> - <help> - <![CDATA[ + <help><![CDATA[ .. class:: infomark **What it does** -The main goal of this tol is to count the number of reads/fragments per exon of each gene in RNA-seq sample. In addition it also prepares your annotation gtf file compatible for counting. +The main goal of this tool is to count the number of reads/fragments per exon of each gene in RNA-seq samples. In addition, it also prepares your annotation GTF file, making it compatible for counting. **Inputs** -Mode-preprare: Takes a normal gtf file as input. For example from ensembl database. -Mode-count: Inputs are flattened gtf file and BAM file. The flattened gtf file can be generated from 'prepare' mode of this tool. +Mode-preprare: Takes a normal gtf file as input. For example from Ensembl database. +Mode-count: Inputs are flattened GTF file and BAM file. The flattened GTF file can be generated from 'prepare' mode of this tool. **Output** -Mode-preprare: Flattened gtf file that contains only exons with corresponding gene ids from given gtf file. Sometimes two or more genes sharing an exon will be merged into an 'aggregate gene' if the aggregate option was used. -Mode-count: Two column tab-delimeted file with exon ids and their read counts. +Mode-prepare: Flattened GTF file that contains only exons with corresponding gene ids from given GTF file. Sometimes two or more genes sharing an exon will be merged into an 'aggregate gene' if the aggregate option was used. +Mode-count: Two column tab-delimited file with exon ids and their read counts. .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html - ]]> - </help> + ]]></help> <citations> <citation type="doi">10.1101/gr.133744.111</citation> </citations> |
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| diff -r f1c406f9554c -r 6e8b61c54ff3 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Jan 28 04:04:39 2018 -0500 |
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| @@ -0,0 +1,15 @@ +<?xml version="1.0"?> +<macros> + <token name="@VERSION@">1.24.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">bioconductor-dexseq</requirement> + <yield /> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.133744.111</citation> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r f1c406f9554c -r 6e8b61c54ff3 test-data/dexseq_result.tabular --- a/test-data/dexseq_result.tabular Sun Jan 29 06:59:35 2017 -0500 +++ b/test-data/dexseq_result.tabular Sun Jan 28 04:04:39 2018 -0500 |
| b |
| b'@@ -1,183 +1,214 @@\n-FBgn0000064:E005\tFBgn0000064\tE005\t859.822533198768\t0.00400580335097871\t103.648404274913\t3.11196699769697e-23\t5.44594224596969e-21\t27.5051135091719\t27.9888903359156\t0.0251544333390813\t3R\t22082655\t22082854\t200\t-\t746\t952\t1227\t542\t790\t802\t722\tFBtr0085000, FBtr0085001, FBtr0084995, FBtr0084994, FBtr0306657, FBtr0114544, FBtr0310661, FBtr0310660, FBtr0084999\n-FBgn0000042:E001\tFBgn0000042\tE001\t963.266257907235\t0.0494674041791383\t58.6864023046738\t1.80471928079693e-13\t1.57912937069731e-11\t29.2361793929567\t27.8104974337299\t-0.0721252413332429\tX\t5794894\t5795046\t153\t+\t3322\t262\t275\t1633\t3139\t244\t129\tFBtr0100662, FBtr0100663, FBtr0070822\n-FBgn0000064:E002\tFBgn0000064\tE002\t7.3266084748515\t0.0174415205517328\t52.6891313145547\t3.61993278740899e-12\t2.11162745932191e-10\t4.57344268891687\t4.36382559042999\t-0.0676871299306827\t3R\t22080926\t22081153\t228\t-\t0\t7\t12\t0\t0\t10\t12\tFBtr0310660, FBtr0084995, FBtr0084994, FBtr0084999\n-FBgn0000084:E003\tFBgn0000084\tE003\t12.7120572355022\t0.0837118156540486\t50.7217207682862\t9.68095672648681e-12\t4.23541856783798e-10\t6.0094928632898\t6.08050302516378\t0.0169474311496155\tX\t20066074\t20066255\t182\t-\t0\t16\t13\t0\t0\t29\t11\tFBtr0070025, FBtr0301931\n-FBgn0000042:E005\tFBgn0000042\tE005\t33.8277404051372\t0.00974672760676001\t34.3730215558909\t3.43552573377072e-08\t1.20243400681975e-06\t9.60659972691163\t11.2480627165693\t0.227578761693847\tX\t5798498\t5798821\t324\t+\t119\t20\t29\t45\t52\t14\t8\tFBtr0100662, FBtr0070823\n-FBgn0000032:E005\tFBgn0000032\tE005\t50.5080907808574\t0.00563866250172629\t33.6728457313117\t4.87567169377265e-08\t1.42207091068369e-06\t11.2003987427418\t11.7345634802096\t0.0672140810963772\t3R\t25818551\t25818649\t99\t-\t42\t53\t56\t38\t55\t45\t53\tFBtr0085609, FBtr0085610\n-FBgn0000117:E003\tFBgn0000117\tE003\t651.648249450539\t0.00646832336464667\t32.2394513365441\t9.98371310442968e-08\t2.49592827610742e-06\t25.6842059292453\t26.4526242482609\t0.0425293818432292\tX\t1788541\t1788813\t273\t-\t676\t728\t799\t493\t606\t574\t569\tFBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988\n-FBgn0000042:E003\tFBgn0000042\tE003\t37923.6657937205\t0.0382188253738751\t28.9809820787994\t5.09166358707019e-07\t9.9004569748587e-06\t51.8034875214762\t51.7296029759846\t-0.0020591075753989\tX\t5796723\t5798206\t1484\t+\t53623\t37301\t41337\t47230\t50144\t22833\t26327\tFBtr0100662, FBtr0100663, FBtr0070822, FBtr0070823\n-FBgn0000117:E004\tFBgn0000117\tE004\t566.705805129229\t0.00396420686097515\t29.062938884796\t4.88723257919492e-07\t9.9004569748587e-06\t25.3467671419344\t24.9167412697074\t-0.0246863519994665\tX\t1788874\t1789074\t201\t-\t541\t507\t690\t417\t761\t498\t535\tFBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988\n-FBgn0000084:E006\tFBgn0000084\tE006\t59.8440945905321\t0.0203559407131398\t22.0440165999181\t1.6338140100348e-05\t0.000285917451756091\t12.8331207213348\t12.5225760471869\t-0.0353406706853485\tX\t20067507\t20067552\t46\t-\t132\t23\t34\t71\t150\t35\t46\tFBtr0070025\n-FBgn0000042:E004\tFBgn0000042\tE004\t2902.21264539337\t0.0406433600957287\t19.0532609703125\t7.28847971089997e-05\t0.00115953086309772\t36.1678574007083\t34.6381912225652\t-0.06234453895514\tX\t5798207\t5798497\t291\t+\t7007\t1635\t1666\t3678\t8835\t1202\t1091\tFBtr0100662, FBtr0100663, FBtr0070823\n-FBgn0000017:E004\tFBgn0000017\tE004\t118.685044393895\t0.009449205970161\t18.6151588688678\t9.07339069495662e-05\t0.00132320280968117\t15.9518565653778\t15.5132175490521\t-0.0402264002183915\t3L\t16619373\t16619627\t255\t-\t103\t108\t87\t107\t162\t144\t104\tFBtr0330133, FBtr0330132, FBtr0330131, FBtr0330130\n-FBgn0000140:E002\tFBgn0000140\tE002\t24.0938527740886\t0.0069964414120799\t18.2356967741571\t0.000109690434972442\t0.00147660200924441\t8.83210929556324\t7.9081263929815\t-0.159422095913981\t3R\t20579850\t20580026\t177\t+\t19\t23\t22\t24\t32\t25\t21\tFBtr0084692\n-FBgn0000064:E011\tFBgn0000064\tE011\t121.014747579775\t0.0162642835242919\t17.7465902170453\t0.000140080246746098\t0.00175100308432622\t17.4845083643665\t14.7073531559126\t-0.249539598513264\t3R\t22086876\t22086879\t4\t-\t154\t77\t97\t210\t219\t76\t86\tFBtr0085001\n-FBgn0000117:E001\tFBgn0000117\tE001\t1110.87821042994\t0.00687680447260985\t17.5318496824093\t0'..b'NA\t2L\t12282514\t12282562\t49\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080344, FBtr0080345, FBtr0331998\n-FBgn0000114:E011\tFBgn0000114\tE011\t0.0883366573889214\t14\t0.0422451536000494\t0.979098942398376\tNA\t0.901165948893395\t0.0127751610731135\t-6.14037941516088\t2L\t12288905\t12289344\t440\t+\t0\t0\t0\t0\t1\t0\t0\tFBtr0080347\n-FBgn0000114:E012\tFBgn0000114\tE012\t0.0933261680585749\t14\t0.0165742552848158\t0.991747115940935\tNA\t0.0161636584595612\t0.822669226222095\t5.66948679957666\t2L\t12298568\t12298749\t182\t+\t1\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998\n FBgn0000114:E013\tFBgn0000114\tE013\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12298814\t12299111\t298\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998\n-FBgn0000114:E014\tFBgn0000114\tE014\t0.0883366573889214\t14\t0.0422451536000494\t0.979098942398376\tNA\t0.901165948893395\t0.0127751610731135\t-6.14037941516088\t2L\t12299188\t12299394\t207\t+\t0\t0\t0\t0\t1\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998\n-FBgn0000114:E015\tFBgn0000114\tE015\t0.0883366573889214\t14\t0.0422451536000494\t0.979098942398376\tNA\t0.901165948893395\t0.0127751610731135\t-6.14037941516088\t2L\t12300361\t12300396\t36\t+\t0\t0\t0\t0\t1\t0\t0\tFBtr0331644\n FBgn0000114:E016\tFBgn0000114\tE016\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12300610\t12300621\t12\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0331644\n FBgn0000114:E017\tFBgn0000114\tE017\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12304446\t12304595\t150\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998\n FBgn0000114:E018\tFBgn0000114\tE018\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12310682\t12311093\t412\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998\n FBgn0000114:E019\tFBgn0000114\tE019\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12311094\t12311104\t11\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331645, FBtr0080347, FBtr0331998\n-FBgn0000116:E002\tFBgn0000116\tE002\t0.0883366573889214\t0.649506832951611\t0.955102166349974\t0.620300597862845\tNA\t1.06977392668418\t0.0168077984590731\t-5.99203136858692\t3L\t9044230\t9044817\t588\t-\t0\t0\t0\t0\t1\t0\t0\tFBtr0331550, FBtr0076546\n-FBgn0000116:E004\tFBgn0000116\tE004\t0.15316821713762\t0.43977187338658\t0.328021702700227\t0.848732811933342\tNA\t0.0232213523500242\t0.90648447279086\t5.2867584097007\t3L\t9046620\t9046661\t42\t-\t0\t0\t1\t0\t0\t0\t0\tFBtr0331550\n-FBgn0000116:E006\tFBgn0000116\tE006\t0.15316821713762\t0.43977187338658\t0.328021702700227\t0.848732811933342\tNA\t0.0232213523500242\t0.90648447279086\t5.2867584097007\t3L\t9055007\t9055567\t561\t-\t0\t0\t1\t0\t0\t0\t0\tFBtr0076543, FBtr0076544\n FBgn0000116:E007\tFBgn0000116\tE007\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t3L\t9055912\t9056048\t137\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0076544\n-FBgn0000116:E008\tFBgn0000116\tE008\t0.205235479273134\t0.353436872439287\t1.98242161309956\t0.371127055796381\tNA\t1.12162424681281\t0.0168071427941747\t-6.06037114417562\t3L\t9057564\t9057617\t54\t-\t0\t0\t0\t0\t0\t1\t0\tFBtr0112791, FBtr0076543\n FBgn0000120:E001\tFBgn0000120\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18078269\t18078496\t228\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n FBgn0000120:E002\tFBgn0000120\tE002\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18078916\t18079723\t808\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n FBgn0000120:E003\tFBgn0000120\tE003\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18079957\t18080086\t130\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n FBgn0000120:E004\tFBgn0000120\tE004\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18080147\t18080415\t269\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n FBgn0000137:E001\tFBgn0000137\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tX\t354533\t357209\t2677\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0070075\n-FBgn0000139:E001\tFBgn0000139\tE001\t0.187795396756122\t0.374758883334333\t0.855539171390518\t0.651961618776603\tNA\t0.887149388069345\t0.0477444815800361\t-4.21577116420462\t3R\t20475810\t20476066\t257\t+\t0\t0\t0\t0\t0\t0\t1\tFBtr0084660\n' |
| b |
| diff -r f1c406f9554c -r 6e8b61c54ff3 test-data/dexseq_result_2fact.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dexseq_result_2fact.tabular Sun Jan 28 04:04:39 2018 -0500 |
| b |
| b'@@ -0,0 +1,307 @@\n+FBgn0000042:E005\tFBgn0000042\tE005\t33.8277404051372\t0.00974669544746392\t12.6851918587988\t0.000368562772095343\t0.0770296193679266\t9.60660113871428\t11.248063753255\t0.552857243884021\tX\t5798498\t5798821\t324\t+\t119\t20\t29\t45\t52\t14\t8\tFBtr0100662, FBtr0070823\n+FBgn0000139:E007\tFBgn0000139\tE007\t17.4740062043893\t0.0174768174826308\t10.9795545088389\t0.000921225722996759\t0.0962680880531613\t8.06219042258468\t5.57421805888543\t-1.16397691752144\t3R\t20478032\t20478312\t281\t+\t12\t5\t9\t24\t28\t24\t19\tFBtr0084660, FBtr0084659, FBtr0306171\n+FBgn0000064:E004\tFBgn0000064\tE004\t27.138007646805\t0.0443836931820446\t9.70272381901728\t0.00183995083792701\t0.128183241708915\t7.41146981322546\t10.6361481097095\t1.21002224137722\t3R\t22082196\t22082345\t150\t-\t74\t30\t39\t9\t25\t20\t9\tFBtr0085000, FBtr0114544\n+FBgn0000053:E004\tFBgn0000053\tE004\t6.32535175423168\t0.045626142883598\t9.02161905056228\t0.00266804962459076\t0.139405592884867\t3.09087219098584\t5.79810451815527\t1.88622972793307\t2L\t7018085\t7018148\t64\t-\t13\t7\t15\t0\t3\t3\t4\tFBtr0100353\n+FBgn0000108:E006\tFBgn0000108\tE006\t0.864384408056277\t0.0838775850414772\t8.17622649197865\t0.00424429612727517\t0.177411578120102\t0.0346924384664682\t2.77171489352896\t12.6628857089353\tX\t465164\t465166\t3\t+\t4\t2\t1\t0\t0\t0\t0\tFBtr0307295, FBtr0307293\n+FBgn0000139:E006\tFBgn0000139\tE006\t30.3520375086607\t0.0116274168067176\t7.51778234858958\t0.00610928459168981\t0.212806746610528\t8.82025966787089\t10.4918896523126\t0.593446583668732\t3R\t20477583\t20477963\t381\t+\t44\t29\t34\t39\t45\t15\t21\tFBtr0084660, FBtr0084659, FBtr0306171\n+FBgn0000064:E011\tFBgn0000064\tE011\t121.014747579775\t0.0162642807531925\t7.07528109396534\t0.00781545601050697\t0.233347186599423\t17.4845079060715\t14.7073531946849\t-0.740648902697183\t3R\t22086876\t22086879\t4\t-\t154\t77\t97\t210\t219\t76\t86\tFBtr0085001\n+FBgn0000100:E001\tFBgn0000100\tE001\t6.87698735532182\t0.0164557487090339\t5.56698102594524\t0.0183022903586644\t0.455054200649313\t4.47698551662587\t5.57993111812181\t0.668156167650007\t3L\t22068967\t22069026\t60\t+\t16\t5\t9\t9\t9\t3\t3\tFBtr0334113\n+FBgn0000139:E004\tFBgn0000139\tE004\t6.44700256941908\t0.0176034247520841\t5.44756371003484\t0.0195956354346594\t0.455054200649313\t4.02487788954067\t5.66490257045217\t1.03311218729944\t3R\t20476902\t20476973\t72\t+\t14\t7\t6\t3\t10\t4\t5\tFBtr0306171\n+FBgn0000097:E003\tFBgn0000097\tE003\t558.924889184516\t0.00477031371166494\t5.18854635674609\t0.0227362260928025\t0.475187125339572\t25.4143298642324\t24.7289690820004\t-0.161815950506053\t2L\t2157427\t2158405\t979\t-\t725\t462\t477\t524\t1052\t491\t412\tFBtr0330658, FBtr0330660, FBtr0077850, FBtr0077851, FBtr0330659\n+FBgn0000053:E006\tFBgn0000053\tE006\t247.836023771802\t0.00263067838891117\t4.96081239277488\t0.0259280236472272\t0.492632449297317\t19.8531147771976\t20.6037362803832\t0.185238337954743\t2L\t7018431\t7019080\t650\t-\t368\t279\t279\t214\t298\t171\t181\tFBtr0079431, FBtr0100353\n+FBgn0000117:E004\tFBgn0000117\tE004\t566.705805129229\t0.00396419762812803\t4.3269149915028\t0.0375141798307434\t0.60531370082316\t25.3467633109321\t24.9167377621243\t-0.101492330264968\tX\t1788874\t1789074\t201\t-\t541\t507\t690\t417\t761\t498\t535\tFBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988\n+FBgn0000140:E002\tFBgn0000140\tE002\t24.0938527740886\t0.00699641461471429\t4.32071532946176\t0.0376510914387611\t0.60531370082316\t8.83211019161567\t7.90812729421176\t-0.363661417457868\t3R\t20579850\t20580026\t177\t+\t19\t23\t22\t24\t32\t25\t21\tFBtr0084692\n+FBgn0000117:E008\tFBgn0000117\tE008\t20.8971168975998\t0.00873563678020118\t3.92015295935667\t0.0477105390847511\t0.702500023104495\t7.84395657324889\t8.88007008822825\t0.408188100799843\tX\t1793414\t1793431\t18\t-\t53\t16\t19\t22\t31\t11\t13\tFBtr0089990, FBtr0089989, FBtr0332583\n+FBgn0000121:E001\tFBgn0000121\tE001\t1.0078404227901\t0.086138824120089\t3.8274806904699\t0.0504186619452987\t0.702500023104495\t1.39252038969136\t2.69308300050152\t1.91892798799308\t3L\t8640361\t8640745\t385\t-\t4\t0\t1\t0\t1\t1\t1\tFBtr0076599\n+FBgn0000017:E003\tFBgn0000017\tE003\t68.6033909674033\t0.0107581511675232\t3.61438663271193\t0.0572818407907794\t0.704229689721935\t13.3760424870186\t12.3288130022102\t-0.310469909507284\t3L\t16616737\t16618374\t1638\t-\t60'..b'3910327521687\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t13012267\t13013887\t1621\t+\t10\t11\t11\t24\t30\t16\t15\tFBtr0086983\n+FBgn0000079:E001\tFBgn0000079\tE001\t84.9770030139345\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t13006211\t13007808\t1598\t-\t44\t51\t53\t78\t132\t115\t99\tFBtr0087004\n+FBgn0000084:E002\tFBgn0000084\tE002\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tX\t20065962\t20065964\t3\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0301931\n+FBgn0000099:E001\tFBgn0000099\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t1593707\t1594728\t1022\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0300505, FBtr0086058, FBtr0086059\n+FBgn0000099:E005\tFBgn0000099\tE005\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t1596431\t1596604\t174\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0300505, FBtr0086058, FBtr0086059, FBtr0300504\n+FBgn0000099:E006\tFBgn0000099\tE006\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t1596664\t1596797\t134\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0086059\n+FBgn0000099:E008\tFBgn0000099\tE008\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t1604294\t1604554\t261\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0300505\n+FBgn0000099:E009\tFBgn0000099\tE009\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t1604787\t1605003\t217\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0086058, FBtr0300504\n+FBgn0000099:E010\tFBgn0000099\tE010\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t1605060\t1605268\t209\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0086058, FBtr0300504\n+FBgn0000099:E011\tFBgn0000099\tE011\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t1605269\t1605271\t3\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0086058\n+FBgn0000099:E012\tFBgn0000099\tE012\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t1613326\t1614335\t1010\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0086058, FBtr0300504\n+FBgn0000114:E001\tFBgn0000114\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12175004\t12175420\t417\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0331998\n+FBgn0000114:E003\tFBgn0000114\tE003\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12205843\t12206130\t288\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0331646, FBtr0080344\n+FBgn0000114:E004\tFBgn0000114\tE004\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12222197\t12222337\t141\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0331647, FBtr0331645\n+FBgn0000114:E007\tFBgn0000114\tE007\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12271591\t12272084\t494\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080344, FBtr0080345, FBtr0331998\n+FBgn0000114:E008\tFBgn0000114\tE008\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12278837\t12278919\t83\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080344, FBtr0080345, FBtr0331998\n+FBgn0000114:E009\tFBgn0000114\tE009\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12282514\t12282562\t49\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080344, FBtr0080345, FBtr0331998\n+FBgn0000114:E013\tFBgn0000114\tE013\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12298814\t12299111\t298\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998\n+FBgn0000114:E016\tFBgn0000114\tE016\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12300610\t12300621\t12\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0331644\n+FBgn0000114:E017\tFBgn0000114\tE017\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12304446\t12304595\t150\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998\n+FBgn0000114:E018\tFBgn0000114\tE018\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12310682\t12311093\t412\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998\n+FBgn0000114:E019\tFBgn0000114\tE019\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t12311094\t12311104\t11\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331645, FBtr0080347, FBtr0331998\n+FBgn0000116:E007\tFBgn0000116\tE007\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t3L\t9055912\t9056048\t137\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0076544\n+FBgn0000120:E001\tFBgn0000120\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18078269\t18078496\t228\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n+FBgn0000120:E002\tFBgn0000120\tE002\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18078916\t18079723\t808\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n+FBgn0000120:E003\tFBgn0000120\tE003\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18079957\t18080086\t130\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n+FBgn0000120:E004\tFBgn0000120\tE004\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2L\t18080147\t18080415\t269\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0307350, FBtr0081030\n+FBgn0000137:E001\tFBgn0000137\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\tX\t354533\t357209\t2677\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0070075\n' |
| b |
| diff -r f1c406f9554c -r 6e8b61c54ff3 test-data/flattened.gtf --- a/test-data/flattened.gtf Sun Jan 29 06:59:35 2017 -0500 +++ b/test-data/flattened.gtf Sun Jan 28 04:04:39 2018 -0500 |
| b |
| b'@@ -1,257 +1,257 @@\n 4\tdexseq_prepare_annotation.py\taggregate_gene\t68336\t77667\t.\t-\t.\tgene_id "FBgn0004859"\n-4\tdexseq_prepare_annotation.py\texonic_part\t68336\t71088\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "001"; gene_id "FBgn0004859"\n-4\tdexseq_prepare_annotation.py\texonic_part\t71142\t71239\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "002"; gene_id "FBgn0004859"\n-4\tdexseq_prepare_annotation.py\texonic_part\t71240\t71306\t.\t-\t.\ttranscripts "FBtr0306168+FBtr0089178"; exonic_part_number "003"; gene_id "FBgn0004859"\n-4\tdexseq_prepare_annotation.py\texonic_part\t71371\t71883\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "004"; gene_id "FBgn0004859"\n-4\tdexseq_prepare_annotation.py\texonic_part\t71940\t72580\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "005"; gene_id "FBgn0004859"\n-4\tdexseq_prepare_annotation.py\texonic_part\t72643\t73010\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "006"; gene_id "FBgn0004859"\n-4\tdexseq_prepare_annotation.py\texonic_part\t76457\t76916\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178"; exonic_part_number "007"; gene_id "FBgn0004859"\n-4\tdexseq_prepare_annotation.py\texonic_part\t76917\t76957\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; exonic_part_number "008"; gene_id "FBgn0004859"\n-4\tdexseq_prepare_annotation.py\texonic_part\t76958\t77667\t.\t-\t.\ttranscripts "FBtr0306168"; exonic_part_number "009"; gene_id "FBgn0004859"\n+4\tdexseq_prepare_annotation.py\texonic_part\t68336\t71088\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "001"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71142\t71239\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "002"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71240\t71306\t.\t-\t.\ttranscripts "FBtr0306168+FBtr0089178"; gene_id "FBgn0004859"; exonic_part_number "003"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71371\t71883\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "004"\n+4\tdexseq_prepare_annotation.py\texonic_part\t71940\t72580\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "005"\n+4\tdexseq_prepare_annotation.py\texonic_part\t72643\t73010\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "006"\n+4\tdexseq_prepare_annotation.py\texonic_part\t76457\t76916\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178"; gene_id "FBgn0004859"; exonic_part_number "007"\n+4\tdexseq_prepare_annotation.py\texonic_part\t76917\t76957\t.\t-\t.\ttranscripts "FBtr0308074+FBtr0089178+FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "008"\n+4\tdexseq_prepare_annotation.py\texonic_part\t76958\t77667\t.\t-\t.\ttranscripts "FBtr0306168"; gene_id "FBgn0004859"; exonic_part_number "009"\n 4\tdexseq_prepare_annotation.py\taggregate_gene\t137015\t150380\t.\t-\t.\tgene_id "FBgn0011747"\n-4\tdexseq_prepare_annotation.py\texonic_part\t137015\t137256\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "001"; gene_id "FBgn0011747"\n-4\tdexseq_prepare_annotation.py\texonic_part\t137312\t139127\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "002"; gene_id "FBgn0011747"\n-4\tdexseq_prepare_annotation.py\texonic_part\t139181\t139405\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "003"; gene_id "FBgn0011747"\n-4\tdexseq_prepare_annotation.py\texonic_part\t139464\t139557\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "004"; gene_id "FBgn0011747"\n-4\tdexseq_prepare_annotation.py\texonic_part\t140514\t140838\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "005"; gene_id "FBgn0011747"\n-4\tdexseq_prepare_annotation.py\texonic_part\t141484\t142425\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; exonic_part_number "006"; gene_id "FBgn0011747"\n-4\tdexseq_prepare_annot'..b'epare_annotation.py\texonic_part\t6402\t8124\t.\t-\t.\ttranscripts "FBtr0100877"; gene_id "FBgn0013684"; exonic_part_number "001"\n dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t8140\t8205\t.\t-\t.\tgene_id "FBgn0013695"\n-dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t8140\t8205\t.\t-\t.\ttranscripts "FBtr0100878"; exonic_part_number "001"; gene_id "FBgn0013695"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t8140\t8205\t.\t-\t.\ttranscripts "FBtr0100878"; gene_id "FBgn0013695"; exonic_part_number "001"\n dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t9837\t9902\t.\t+\t.\tgene_id "FBgn0013707"\n-dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9837\t9902\t.\t+\t.\ttranscripts "FBtr0100881"; exonic_part_number "001"; gene_id "FBgn0013707"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9837\t9902\t.\t+\t.\ttranscripts "FBtr0100881"; gene_id "FBgn0013707"; exonic_part_number "001"\n dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t9903\t9963\t.\t-\t.\tgene_id "FBgn0013702"\n-dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9903\t9963\t.\t-\t.\ttranscripts "FBtr0100882"; exonic_part_number "001"; gene_id "FBgn0013702"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9903\t9963\t.\t-\t.\ttranscripts "FBtr0100882"; gene_id "FBgn0013702"; exonic_part_number "001"\n dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t9970\t10494\t.\t+\t.\tgene_id "FBgn0013685"\n-dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9970\t10494\t.\t+\t.\ttranscripts "FBtr0100883"; exonic_part_number "001"; gene_id "FBgn0013685"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t9970\t10494\t.\t+\t.\ttranscripts "FBtr0100883"; gene_id "FBgn0013685"; exonic_part_number "001"\n dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t10498\t11634\t.\t+\t.\tgene_id "FBgn0013678"\n-dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t10498\t11634\t.\t+\t.\ttranscripts "FBtr0100884"; exonic_part_number "001"; gene_id "FBgn0013678"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t10498\t11634\t.\t+\t.\ttranscripts "FBtr0100884"; gene_id "FBgn0013678"; exonic_part_number "001"\n dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t11637\t11702\t.\t+\t.\tgene_id "FBgn0013706"\n-dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t11637\t11702\t.\t+\t.\ttranscripts "FBtr0100885"; exonic_part_number "001"; gene_id "FBgn0013706"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t11637\t11702\t.\t+\t.\ttranscripts "FBtr0100885"; gene_id "FBgn0013706"; exonic_part_number "001"\n dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t11720\t12658\t.\t-\t.\tgene_id "FBgn0013679"\n-dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t11720\t12658\t.\t-\t.\ttranscripts "FBtr0100886"; exonic_part_number "001"; gene_id "FBgn0013679"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t11720\t12658\t.\t-\t.\ttranscripts "FBtr0100886"; gene_id "FBgn0013679"; exonic_part_number "001"\n dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t12669\t12733\t.\t-\t.\tgene_id "FBgn0013698"\n-dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t12669\t12733\t.\t-\t.\ttranscripts "FBtr0100887"; exonic_part_number "001"; gene_id "FBgn0013698"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t12669\t12733\t.\t-\t.\ttranscripts "FBtr0100887"; gene_id "FBgn0013698"; exonic_part_number "001"\n dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\taggregate_gene\t14131\t14916\t.\t-\t.\tgene_id "FBgn0013688"\n-dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t14131\t14916\t.\t-\t.\ttranscripts "FBtr0100890"; exonic_part_number "001"; gene_id "FBgn0013688"\n+dmel_mitochondrion_genome\tdexseq_prepare_annotation.py\texonic_part\t14131\t14916\t.\t-\t.\ttranscripts "FBtr0100890"; gene_id "FBgn0013688"; exonic_part_number "001"\n' |