| Previous changeset 3:f89c9b25feb4 (2018-07-28) Next changeset 5:278b189248cd (2019-01-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf |
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modified:
dexseq.xml dexseq_count.xml macros.xml test-data/dexseq_result.tabular test-data/dexseq_result_2fact.tabular test-data/flattened.gtf test-data/original.gtf test-data/out_count.tab |
| b |
| diff -r f89c9b25feb4 -r 251393b72616 dexseq.xml --- a/dexseq.xml Sat Jul 28 03:44:02 2018 -0400 +++ b/dexseq.xml Tue Dec 11 00:19:18 2018 -0500 |
| [ |
| @@ -1,26 +1,26 @@ <tool id="dexseq" name="DEXSeq" version="@VERSION@.0"> <description>Determines differential exon usage from count tables</description> - <macros> + <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> + <requirement type="package" version="1.20.2">r-getopt</requirement> + <requirement type="package" version="0.2.20">r-rjson</requirement> </expand> <code file="dexseq_helper.py" /> <stdio> <regex match="Execution halted" - source="both" - level="fatal" - description="Execution halted." /> + source="both" + level="fatal" + description="Execution halted." /> <regex match="Input-Error 01" - source="both" - level="fatal" - description="Error in your input parameters: Make sure you only apply factors to selected samples." /> + source="both" + level="fatal" + description="Error in your input parameters: Make sure you only apply factors to selected samples." /> <regex match="Error in" - source="both" - level="fatal" - description="An undefined error occured, please check your input carefully and contact your administrator." /> + source="both" + level="fatal" + description="An undefined error occured, please check your input carefully and contact your administrator." /> <regex match="Error:" source="both" level="fatal" @@ -96,8 +96,8 @@ <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/> </inputs> <outputs> - <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}" /> - <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}"> + <data name="dexseq_out" format="tabular" label="DEXSeq result file on ${on_string}" /> + <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}"> <filter>report is True</filter> </data> </outputs> @@ -114,7 +114,7 @@ </repeat> <param name="report" value="False"/> <param name="fdr_cutoff" value="1"/> - <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/> + <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/> </test> <!-- Ensure report works--> <test expect_num_outputs="2"> @@ -128,7 +128,7 @@ </repeat> <param name="report" value="True"/> <param name="fdr_cutoff" value="1"/> - <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular"/> + <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/> </test> <!-- Ensure two factors works--> <test expect_num_outputs="1"> @@ -149,7 +149,7 @@ </repeat> <param name="report" value="False"/> <param name="fdr_cutoff" value="0.05"/> - <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular"/> + <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular" compare="sim_size"/> </test> </tests> <help><![CDATA[ @@ -163,10 +163,10 @@ **Inputs** 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. 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. +DEXSeq_ is capable of handling multiple factors that affect your experiment. The first factor you input is considered to be the primary +factor that affects gene expressions. You can also input several secondary factors that might +influence your experiment but the final output will be changes in genes due to primary factor in the presence of secondary factors. Each factor has two levels/states. +You need to select an appropriate count table from your history for each factor level. The following table gives some examples of factors and their levels: @@ -184,7 +184,7 @@ Gender Female Male ========= ============== =============== -*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level2. Here the order of factor levels is important. For example, for the factor 'condition' given in above table, DEXSeq computes fold changes of 'Knockdown' samples against 'Wildtype', i.e. the values correspond to up or down regulations of genes in Knockdown samples. +*Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level 2. Here the order of factor levels is important. For example, for the factor 'condition' given in the above table, DEXSeq computes fold changes of 'Knockdown' samples against 'Wildtype', i.e. the values correspond to up or down regulations of genes in Knockdown samples. **Output** |
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| diff -r f89c9b25feb4 -r 251393b72616 dexseq_count.xml --- a/dexseq_count.xml Sat Jul 28 03:44:02 2018 -0400 +++ b/dexseq_count.xml Tue Dec 11 00:19:18 2018 -0500 |
| [ |
| @@ -4,7 +4,6 @@ <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 --> @@ -22,11 +21,11 @@ '$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 + --format bam + --paired $mode.paired + --stranded $mode.stranded + --minaqual $mode.qual + --order $mode.order $mode.flattened_gtf_in '$mode.bamfile' '$counts_file' @@ -47,15 +46,15 @@ <when value="count"> <param name="bamfile" type="data" format="bam" label="Input bam file"/> <param name="flattened_gtf_in" type="data" format="gff" label="DEXSeq compatible GTF file" help="Created by prepare mode"/> - <param name="paired" type="boolean" checked="True" truevalue="yes" falsevalue="no" label="Is libray paired end?"/> + <param name="paired" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Is library paired end?"/> <param name="stranded" type="select" label="Is library strand specific?"> + <option value="yes" selected="true">Yes</option> <option value="no">No</option> - <option value="yes">Yes</option> <option value="reverse">Yes, but reverse</option> </param> <param name="qual" type="integer" value="10" label="Skip all reads with alignment quality lower than the given minimum value"/> <param name="order" type="select" label="Sorting order of alignments" help="If you generated your alignments using tophat, they are by default position sorted. Ignored for single-end data"> - <option value="pos">By position</option> + <option value="pos" selected="true">By position</option> <option value="name">By name</option> </param> </when> @@ -63,10 +62,10 @@ </inputs> <outputs> - <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}"> + <data name="counts_file" format="tabular" label="DEXSeq count reads on ${on_string}"> <filter>mode['mode_select'] == 'count'</filter> </data> - <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation on ${on_string}"> + <data name="flattened_gtf_out" format="gtf" label="DEXSeq prepare annotation on ${on_string}"> <filter>mode['mode_select'] == 'prepare'</filter> </data> </outputs> @@ -83,6 +82,7 @@ <param name="mode_select" value="count" /> <param name="bamfile" ftype="bam" value="in.bam" /> <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/> + <param name="stranded" value="no" /> <output name="counts_file" ftype="tabular" file="out_count.tab"/> </test> </tests> @@ -97,12 +97,12 @@ **Inputs** -Mode-preprare: Takes a normal gtf file as input. For example from Ensembl database. +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-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-prepare: Flattened GTF file that contains only exons with corresponding gene ids from the input 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 |
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| diff -r f89c9b25feb4 -r 251393b72616 macros.xml --- a/macros.xml Sat Jul 28 03:44:02 2018 -0400 +++ b/macros.xml Tue Dec 11 00:19:18 2018 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">1.24.0</token> + <token name="@VERSION@">1.26.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">bioconductor-dexseq</requirement> |
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| diff -r f89c9b25feb4 -r 251393b72616 test-data/dexseq_result.tabular --- a/test-data/dexseq_result.tabular Sat Jul 28 03:44:02 2018 -0400 +++ b/test-data/dexseq_result.tabular Tue Dec 11 00:19:18 2018 -0500 |
| b |
| b'@@ -1,212 +1,212 @@\n-FBgn0000053:E004\tFBgn0000053\tE004\t6.32535175423168\t0.0260746424475031\t12.5307991355525\t0.000400298568832247\t0.0509854212431317\t0.560431605940778\t1.03559156651448\t1.90324657834009\t2L\t7018085\t7018148\t64\t-\t13\t7\t15\t0\t3\t3\t4\tFBtr0100353\n-FBgn0000064:E004\tFBgn0000064\tE004\t27.138007646805\t0.0320614216225203\t12.161356622295\t0.000487898767876859\t0.0509854212431317\t1.2459178514709\t1.60494807035688\t1.24070300138052\t3R\t22082196\t22082345\t150\t-\t74\t30\t39\t9\t25\t20\t9\tFBtr0085000, FBtr0114544\n-FBgn0000139:E007\tFBgn0000139\tE007\t17.4740062043893\t0.0165626680599344\t10.7326356817656\t0.00105262408773491\t0.0733328114455321\t1.32932184328664\t1.0013182867392\t-1.17190187035822\t3R\t20478032\t20478312\t281\t+\t12\t5\t9\t24\t28\t24\t19\tFBtr0084660, FBtr0084659, FBtr0306171\n-FBgn0000108:E006\tFBgn0000108\tE006\t0.864384408056277\t0.0398325102744689\t8.77610443776344\t0.00305202304945237\t0.159468204333886\t0.000374560319648285\t0.49804148955328\t11.2816645926407\tX\t465164\t465166\t3\t+\t4\t2\t1\t0\t0\t0\t0\tFBtr0307295, FBtr0307293\n-FBgn0000139:E006\tFBgn0000139\tE006\t30.3520375086607\t0.012150441933916\t6.45968249150421\t0.0110349360712362\t0.461260327777674\t1.41506098745029\t1.58548201524133\t0.58473231982979\t3R\t20477583\t20477963\t381\t+\t44\t29\t34\t39\t45\t15\t21\tFBtr0084660, FBtr0084659, FBtr0306171\n-FBgn0000024:E009\tFBgn0000024\tE009\t0.979078995544713\t0.0565367642678669\t4.4548767766085\t0.0348017269675052\t0.661232812382599\t0.116350866727098\t0.386493846881178\t2.22364698487279\t3R\t9071532\t9072376\t845\t-\t1\t2\t3\t0\t1\t0\t0\tFBtr0082780, FBtr0300486\n-FBgn0000053:E006\tFBgn0000053\tE006\t247.836023771802\t0.00413151745892372\t4.77583288596006\t0.0288618820540252\t0.661232812382599\t2.36309348197775\t2.42244720768454\t0.197970803636516\t2L\t7018431\t7019080\t650\t-\t368\t279\t279\t214\t298\t171\t181\tFBtr0079431, FBtr0100353\n-FBgn0000064:E011\tFBgn0000064\tE011\t121.014747579775\t0.0367036950530367\t4.95296446215627\t0.0260459705193723\t0.661232812382599\t2.17850465324405\t1.96568838553701\t-0.713061914467984\t3R\t22086876\t22086879\t4\t-\t154\t77\t97\t210\t219\t76\t86\tFBtr0085001\n-FBgn0000083:E008\tFBgn0000083\tE008\t148.254009682968\t0.0362541326904268\t4.8286706233263\t0.0279902049680463\t0.661232812382599\t2.0871809472773\t2.26370055995136\t0.590354614237569\t3R\t16896446\t16896639\t194\t+\t317\t119\t178\t86\t149\t110\t129\tFBtr0089518, FBtr0089520\n-FBgn0000100:E001\tFBgn0000100\tE001\t6.87698735532182\t0.0156911579144217\t4.46398826406511\t0.0346165842296028\t0.661232812382599\t0.834776472273814\t0.995293998312963\t0.607664158805536\t3L\t22068967\t22069026\t60\t+\t16\t5\t9\t9\t9\t3\t3\tFBtr0334113\n-FBgn0000139:E004\tFBgn0000139\tE004\t6.44700256941908\t0.0145422977178803\t5.41652106099627\t0.0199470669107782\t0.661232812382599\t0.747955825645429\t1.01499858139933\t1.02448572935067\t3R\t20476902\t20476973\t72\t+\t14\t7\t6\t3\t10\t4\t5\tFBtr0306171\n-FBgn0000121:E001\tFBgn0000121\tE001\t1.0078404227901\t0.0424259836702434\t4.23409707141566\t0.0396196923685856\t0.690042975419532\t0.184461693322922\t0.483143408154597\t1.94804462100918\t3L\t8640361\t8640745\t385\t-\t4\t0\t1\t0\t1\t1\t1\tFBtr0076599\n-FBgn0000121:E003\tFBgn0000121\tE003\t2.30524126345099\t0.0402440115149809\t3.75442763887364\t0.0526678244950707\t0.846736563036136\t0.591875192812152\t0.349324665312964\t-1.234878553517\t3L\t8641070\t8642036\t967\t-\t2\t0\t1\t3\t11\t2\t1\tFBtr0076599\n-FBgn0000140:E005\tFBgn0000140\tE005\t32.5533299591785\t0.0160636446563194\t3.62937433561051\t0.0567681538331465\t0.847467439366259\t1.47442818436125\t1.58463861123828\t0.377289446539178\t3R\t20585313\t20585614\t302\t+\t51\t37\t38\t35\t47\t22\t13\tFBtr0084692\n-FBgn0000053:E002\tFBgn0000053\tE002\t211.729712208868\t0.00784998742581861\t3.19129190493953\t0.0740314840145184\t0.910151774060844\t2.36279193806629\t2.2848997064752\t-0.259987469644205\t2L\t7016437\t7017486\t1050\t-\t295\t164\t223\t247\t282\t155\t176\tFBtr0079431\n-FBgn0000061:E005\tFBgn0000061\tE005\t0.374447732873272\t0.0928459054977042\t3.23037987882481\t0.0722839193917796\t0.910151774060844\t0.107605853514733\t0.179667226272506\t0.865847002074158\t2L\t386703\t387439\t737\t+\t2\t0\t0\t0\t0\t0\t1\tFBtr0078053\n-FBgn0000119:E003\tFBgn0000119\tE003\t13.5729072769284\t0.0112702871460675\t3.388307324835\t0.0656603232106756\t0.91015177'..b', FBtr0089989\n+FBgn0000119:E001\tFBgn0000119\tE001\t71.3729832029852\t0.0159624632627942\t0.0269667420330393\t0.869561471727217\t0.988468250475379\t1.85920516847074\t1.86706491111384\t0.0264722960489339\t2R\t9341159\t9342741\t1583\t-\t126\t62\t49\t77\t133\t44\t57\tFBtr0087702\n+FBgn0000119:E005\tFBgn0000119\tE005\t187.898456532462\t0.013267575291108\t0.0961366249497075\t0.756516039204156\t0.988468250475379\t2.27814423475712\t2.26281595528504\t-0.0511940813733096\t2R\t9344041\t9347030\t2990\t-\t264\t142\t176\t218\t266\t139\t168\tFBtr0087702\n+FBgn0000119:E006\tFBgn0000119\tE006\t13.655959120889\t0.0317708574435141\t0.0356101319975579\t0.850322880004392\t0.988468250475379\t1.1568164959252\t1.18987131201111\t0.117704678772041\t2R\t9369281\t9369589\t309\t-\t31\t8\t9\t13\t22\t14\t8\tFBtr0087702\n+FBgn0000121:E002\tFBgn0000121\tE002\t1.2324267524932\t0.0533181349969619\t0.0494801272337142\t0.823970372532986\t0.988468250475379\t0.314309343104816\t0.349279685845567\t0.217606855982165\t3L\t8640808\t8641002\t195\t-\t2\t1\t0\t3\t1\t1\t1\tFBtr0076599\n+FBgn0000139:E001\tFBgn0000139\tE001\t0.187795396756122\t0.0871311030435317\t0.149285553223777\t0.699219046204095\t0.988468250475379\t0.08311138014973\t0.000263871425191593\t-8.43887461912595\t3R\t20475810\t20476066\t257\t+\t0\t0\t0\t0\t0\t0\t1\tFBtr0084660\n+FBgn0000139:E002\tFBgn0000139\tE002\t1.96739811366688\t0.129053704862598\t0.162639743479019\t0.686737706815857\t0.988468250475379\t0.473951278180885\t0.532675374661105\t0.284486402504392\t3R\t20476127\t20476311\t185\t+\t4\t3\t0\t2\t7\t1\t0\tFBtr0084660\n+FBgn0000139:E003\tFBgn0000139\tE003\t3.61191788404307\t0.0958517409025262\t0.306843426224418\t0.579623675618226\t0.988468250475379\t0.658195763389358\t0.734052813700759\t0.315660456533852\t3R\t20476372\t20476716\t345\t+\t8\t4\t1\t3\t12\t1\t2\tFBtr0084660\n+FBgn0000139:E009\tFBgn0000139\tE009\t96.3385782859831\t0.0114312071603566\t0.248295374913951\t0.618277922077528\t0.988468250475379\t1.97768176633948\t1.9519796177073\t-0.0863168051306058\t3R\t20478820\t20479098\t279\t+\t92\t64\t93\t95\t166\t87\t94\tFBtr0084660, FBtr0084659, FBtr0306171\n+FBgn0000140:E001\tFBgn0000140\tE001\t10.7470539964813\t0.0236213886915515\t0.058774620002751\t0.808443291557068\t0.988468250475379\t1.10752884322106\t1.0423311673325\t-0.236506910881205\t3R\t20579625\t20579777\t153\t+\t14\t9\t11\t21\t17\t5\t5\tFBtr0084692\n+FBgn0000140:E003\tFBgn0000140\tE003\t26.5896581030249\t0.0914989054318421\t0.160703130466203\t0.688509985157294\t0.988468250475379\t1.47243744241299\t1.37191492727433\t-0.347090255979845\t3R\t20580079\t20580291\t213\t+\t27\t25\t22\t29\t20\t32\t23\tFBtr0084692\n+FBgn0000140:E004\tFBgn0000140\tE004\t396.131203959444\t0.0294670271521804\t0.119915668147684\t0.729125972221598\t0.988468250475379\t2.61535281828511\t2.58420339546523\t-0.103736907472117\t3R\t20580371\t20585252\t4882\t+\t717\t355\t274\t503\t729\t250\t241\tFBtr0084692\n+FBgn0000083:E005\tFBgn0000083\tE005\t519.429405568491\t0.016962147011311\t0.000633291146755255\t0.979923133432178\t0.994193858676336\t2.71639748619056\t2.708785741171\t-0.0253347752316291\t3R\t16894560\t16894741\t182\t+\t567\t413\t615\t536\t584\t399\t524\tFBtr0089518, FBtr0089519, FBtr0089520, FBtr0089517\n+FBgn0000052:E003\tFBgn0000052\tE003\t314.320768507933\t0.0159335145712051\t0.000170508834514749\t0.989581596757519\t0.999142771605418\t2.49025417438327\t2.49234631399963\t0.00697243229160804\t2L\t6044428\t6045526\t1099\t-\t343\t283\t295\t346\t457\t261\t265\tFBtr0079219, FBtr0079221, FBtr0079220\n+FBgn0000116:E004\tFBgn0000116\tE004\t0.15316821713762\t0.09618129180048\t-0.0994480190303477\t1\t1\t5.79567992666157e-05\t0.0848430094196974\t10.6587205272148\t3L\t9046620\t9046661\t42\t-\t0\t0\t1\t0\t0\t0\t0\tFBtr0331550\n+FBgn0000116:E006\tFBgn0000116\tE006\t0.15316821713762\t0.09618129180048\t-0.0994480190303477\t1\t1\t5.79567992666157e-05\t0.0848430094196972\t10.6587205272148\t3L\t9055007\t9055567\t561\t-\t0\t0\t1\t0\t0\t0\t0\tFBtr0076543, FBtr0076544\n FBgn0000003:E001\tFBgn0000003\tE001\t0.15316821713762\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t3R\t2648220\t2648518\t299\t+\t0\t0\t1\t0\t0\t0\t0\tFBtr0081624\n FBgn0000008:E001\tFBgn0000008\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t18024494\t18024495\t2\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0100521\n FBgn0000014:E002\tFBgn0000014\tE002\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t3R\t12633349\t12635783\t2435\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0083387, FBtr0306337, FBtr0300485, FBtr0083388\n' |
| b |
| diff -r f89c9b25feb4 -r 251393b72616 test-data/dexseq_result_2fact.tabular --- a/test-data/dexseq_result_2fact.tabular Sat Jul 28 03:44:02 2018 -0400 +++ b/test-data/dexseq_result_2fact.tabular Tue Dec 11 00:19:18 2018 -0500 |
| b |
| b'@@ -1,212 +1,212 @@\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-\t'..b'16\t-12.2835519633586\t2L\t12288905\t12289344\t440\t+\t0\t0\t0\t0\t1\t0\t0\tFBtr0080347\n+FBgn0000114:E012\tFBgn0000114\tE012\t0.0933261680585749\t14\t0.0151245147496439\t0.902121537033148\t1\t0.0161618280469575\t0.822650605971438\t11.3412504567185\t2L\t12298568\t12298749\t182\t+\t1\t0\t0\t0\t0\t0\t0\tFBtr0300567, FBtr0331648, FBtr0331646, FBtr0331647, FBtr0331644, FBtr0331645, FBtr0080347, FBtr0080344, FBtr0080345, FBtr0331998\n+FBgn0000114:E014\tFBgn0000114\tE014\t0.0883366573889214\t14\t0.0384681766311132\t0.844506021806725\t1\t0.901163184517619\t0.01277346475716\t-12.2835519633586\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\t0.0384681766311132\t0.844506021806725\t1\t0.901163184517619\t0.01277346475716\t-12.2835519633586\t2L\t12300361\t12300396\t36\t+\t0\t0\t0\t0\t1\t0\t0\tFBtr0331644\n+FBgn0000116:E004\tFBgn0000116\tE004\t0.15316821713762\t0.439815447670541\t-0.0700042811025554\t1\t1\t0.0232209004275195\t0.906477229392129\t10.5759962391689\t3L\t9046620\t9046661\t42\t-\t0\t0\t1\t0\t0\t0\t0\tFBtr0331550\n+FBgn0000116:E005\tFBgn0000116\tE005\t1.25599426711867\t0.472104568434921\t-0.00158843673641229\t1\t1\t2.0953395114146\t2.24506163576219\t0.201074602752124\t3L\t9050643\t9050681\t39\t-\t1\t0\t5\t1\t3\t0\t0\tFBtr0076545\n+FBgn0000116:E006\tFBgn0000116\tE006\t0.15316821713762\t0.439815447670541\t-0.0700042811025554\t1\t1\t0.0232209004275212\t0.906477229392129\t10.5759962391685\t3L\t9055007\t9055567\t561\t-\t0\t0\t1\t0\t0\t0\t0\tFBtr0076543, FBtr0076544\n+FBgn0000117:E006\tFBgn0000117\tE006\t156.240420394897\t0.0085542074356747\t0.0189649087814985\t0.890467134556043\t1\t17.7254675674669\t17.5451703485226\t-0.0463878438247756\tX\t1793013\t1793072\t60\t-\t198\t147\t167\t179\t242\t93\t124\tFBtr0089990, FBtr0089991, FBtr0089992, FBtr0332583, FBtr0089989, FBtr0089988\n+FBgn0000117:E007\tFBgn0000117\tE007\t4.5734995655629\t0.0692028953471076\t0.13944050372217\t0.70883786195167\t1\t4.27081682130186\t4.15200594359431\t-0.0843671596411597\tX\t1793337\t1793413\t77\t-\t10\t5\t2\t3\t15\t1\t3\tFBtr0332583\n+FBgn0000117:E009\tFBgn0000117\tE009\t75.1849884692702\t0.0237530624974545\t0.0129029846694664\t0.909561779999495\t1\t13.9202742735026\t13.550906840725\t-0.105708824655276\tX\t1793432\t1793557\t126\t-\t102\t64\t78\t105\t107\t37\t64\tFBtr0332583, FBtr0089990, FBtr0089989, FBtr0089988\n+FBgn0000117:E010\tFBgn0000117\tE010\t42.7651357723149\t0.0146658777705333\t0.0255392433549844\t0.873030728587431\t1\t11.366144418293\t10.9161877955769\t-0.144993437862887\tX\t1793558\t1793643\t86\t-\t87\t32\t27\t58\t69\t27\t31\tFBtr0089990, FBtr0089989\n+FBgn0000119:E001\tFBgn0000119\tE001\t71.3729832029852\t0.0111382575170043\t0.188041060651543\t0.664552051202675\t1\t13.476054977176\t13.5892329009486\t0.0326352901711147\t2R\t9341159\t9342741\t1583\t-\t126\t62\t49\t77\t133\t44\t57\tFBtr0087702\n+FBgn0000119:E006\tFBgn0000119\tE006\t13.655959120889\t0.037494635364515\t0.0687714227743044\t0.793134057224867\t1\t6.67105868946973\t6.92210999295732\t0.116571475051037\t2R\t9369281\t9369589\t309\t-\t31\t8\t9\t13\t22\t14\t8\tFBtr0087702\n+FBgn0000121:E002\tFBgn0000121\tE002\t1.2324267524932\t0.147712274149084\t0.0344325243825381\t0.852789801284774\t1\t1.97474437554829\t2.1046084985034\t0.185347718172468\t3L\t8640808\t8641002\t195\t-\t2\t1\t0\t3\t1\t1\t1\tFBtr0076599\n+FBgn0000140:E001\tFBgn0000140\tE001\t10.7470539964813\t0.0364725623871334\t0.00683299191858566\t0.93412036993095\t1\t6.2315093452018\t5.91337033650988\t-0.162542764874986\t3R\t20579625\t20579777\t153\t+\t14\t9\t11\t21\t17\t5\t5\tFBtr0084692\n+FBgn0000140:E004\tFBgn0000140\tE004\t396.131203959444\t0.00847249449173582\t3.17630525898949e-05\t0.995503248592858\t1\t23.2122607370292\t23.0392443785726\t-0.0414131306443135\t3R\t20580371\t20585252\t4882\t+\t717\t355\t274\t503\t729\t250\t241\tFBtr0084692\n FBgn0000003:E001\tFBgn0000003\tE001\t0.15316821713762\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t3R\t2648220\t2648518\t299\t+\t0\t0\t1\t0\t0\t0\t0\tFBtr0081624\n FBgn0000008:E001\tFBgn0000008\tE001\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t2R\t18024494\t18024495\t2\t+\t0\t0\t0\t0\t0\t0\t0\tFBtr0100521\n FBgn0000014:E002\tFBgn0000014\tE002\t0\tNA\tNA\tNA\tNA\tNA\tNA\tNA\t3R\t12633349\t12635783\t2435\t-\t0\t0\t0\t0\t0\t0\t0\tFBtr0083387, FBtr0306337, FBtr0300485, FBtr0083388\n' |
| b |
| diff -r f89c9b25feb4 -r 251393b72616 test-data/flattened.gtf --- a/test-data/flattened.gtf Sat Jul 28 03:44:02 2018 -0400 +++ b/test-data/flattened.gtf Tue Dec 11 00:19:18 2018 -0500 |
| b |
| b'@@ -1,257 +1,281 @@\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"; 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"; gene_id "FBgn0011747"; exonic_part_number "001"\n-4\tdexseq_prepare_annotation.py\texonic_part\t137312\t139127\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "002"\n-4\tdexseq_prepare_annotation.py\texonic_part\t139181\t139405\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "003"\n-4\tdexseq_prepare_annotation.py\texonic_part\t139464\t139557\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "004"\n-4\tdexseq_prepare_annotation.py\texonic_part\t140514\t140838\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "005"\n-4\tdexseq_prepare_annotation.py\texonic_part\t141484\t142425\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "006"\n-4\tdexseq_prepare_annotation.py\texonic_part\t142479\t142582\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "007"\n-4\tdexseq_prepare_annotation.py\texonic_part\t142935\t144048\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "008"\n-4\tdexseq_prepare_annotation.py\texonic_part\t144411\t144518\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "009"\n-4\tdexseq_prepare_annotation.py\texonic_part\t149948\t150068\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089173+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "010"\n-4\tdexseq_prepare_annotation.py\texonic_part\t150069\t150078\t.\t-\t.\ttranscripts "FBtr0089173"; gene_id "FBgn0011747"; exonic_part_number "011"\n-4\tdexseq_prepare_annotation.py\texonic_part\t150181\t150353\t.\t-\t.\ttranscripts "FBtr0089172"; gene_id "FBgn0011747"; exonic_part_number "012"\n-4\tdexseq_prepare_annotation.py\texonic_part\t150354\t150380\t.\t-\t.\ttranscripts "FBtr0089172+FBtr0089171"; gene_id "FBgn0011747"; exonic_part_number "013"\n-4\tdexseq_prepare_annotation.py\taggregate_gene\t522436\t560418\t.\t+\t.\tgene_id "FBgn0004607"\n-4\tdexseq_prepare_annotation.py\texonic_part\t522436\t522483\t.\t+\t.\ttranscripts "FBtr0332913+FBtr0089070+FBtr0307167"; gene_id "FBgn0004607"; exonic_part_number "001"\n-4\tdexseq_prepare_annotation.py\texonic_part\t524477\t524764\t.\t+\t.\ttranscripts "FBtr0332913+FB'..b'Bgn0004648"\n+X\tdexseq_prepare_annotation.py\texonic_part\t396869\t396969\t.\t+\t.\ttranscripts "FBtr0290017+FBtr0290016+FBtr0070086+FBtr0070087+FBtr0070084+FBtr0070085+FBtr0070083+FBtr0070081"; exonic_part_number "007"; gene_id "FBgn0004648"\n+X\tdexseq_prepare_annotation.py\texonic_part\t396970\t398365\t.\t+\t.\ttranscripts "FBtr0070086+FBtr0070085"; exonic_part_number "008"; gene_id "FBgn0004648"\n+X\tdexseq_prepare_annotation.py\texonic_part\t398701\t398818\t.\t+\t.\ttranscripts "FBtr0290017+FBtr0290016+FBtr0070087+FBtr0070084+FBtr0070083+FBtr0070081"; exonic_part_number "009"; gene_id "FBgn0004648"\n+X\tdexseq_prepare_annotation.py\texonic_part\t398949\t400275\t.\t+\t.\ttranscripts "FBtr0290017+FBtr0290016+FBtr0070087+FBtr0070084+FBtr0070083+FBtr0070081"; exonic_part_number "010"; gene_id "FBgn0004648"\n+X\tdexseq_prepare_annotation.py\texonic_part\t400341\t400564\t.\t+\t.\ttranscripts "FBtr0290017+FBtr0290016+FBtr0070087+FBtr0070084+FBtr0070083+FBtr0070081"; exonic_part_number "011"; gene_id "FBgn0004648"\n+X\tdexseq_prepare_annotation.py\texonic_part\t400632\t401839\t.\t+\t.\ttranscripts "FBtr0290017+FBtr0290016+FBtr0070087+FBtr0070084+FBtr0070083+FBtr0070081"; exonic_part_number "012"; gene_id "FBgn0004648"\n+X\tdexseq_prepare_annotation.py\texonic_part\t401840\t401901\t.\t+\t.\ttranscripts "FBtr0070084+FBtr0070083+FBtr0070081"; exonic_part_number "013"; gene_id "FBgn0004648"\n+X\tdexseq_prepare_annotation.py\texonic_part\t401902\t402467\t.\t+\t.\ttranscripts "FBtr0290017+FBtr0290016+FBtr0070087+FBtr0070084+FBtr0070083+FBtr0070081"; exonic_part_number "014"; gene_id "FBgn0004648"\n+X\tdexseq_prepare_annotation.py\texonic_part\t402468\t403113\t.\t+\t.\ttranscripts "FBtr0070087+FBtr0070084+FBtr0070081+FBtr0070083+FBtr0290016"; exonic_part_number "015"; gene_id "FBgn0004648"\n+X\tdexseq_prepare_annotation.py\taggregate_gene\t403451\t422067\t.\t+\t.\tgene_id "FBgn0023535"\n+X\tdexseq_prepare_annotation.py\texonic_part\t403451\t403467\t.\t+\t.\ttranscripts "FBtr0070088"; exonic_part_number "001"; gene_id "FBgn0023535"\n+X\tdexseq_prepare_annotation.py\texonic_part\t403468\t403749\t.\t+\t.\ttranscripts "FBtr0333318+FBtr0070088"; exonic_part_number "002"; gene_id "FBgn0023535"\n+X\tdexseq_prepare_annotation.py\texonic_part\t403943\t404146\t.\t+\t.\ttranscripts "FBtr0333318+FBtr0070088"; exonic_part_number "003"; gene_id "FBgn0023535"\n+X\tdexseq_prepare_annotation.py\texonic_part\t404208\t404394\t.\t+\t.\ttranscripts "FBtr0333318+FBtr0070088"; exonic_part_number "004"; gene_id "FBgn0023535"\n+X\tdexseq_prepare_annotation.py\texonic_part\t420339\t420534\t.\t+\t.\ttranscripts "FBtr0333318"; exonic_part_number "005"; gene_id "FBgn0023535"\n+X\tdexseq_prepare_annotation.py\texonic_part\t420535\t420634\t.\t+\t.\ttranscripts "FBtr0333318+FBtr0070088"; exonic_part_number "006"; gene_id "FBgn0023535"\n+X\tdexseq_prepare_annotation.py\texonic_part\t421592\t422061\t.\t+\t.\ttranscripts "FBtr0333318+FBtr0070088"; exonic_part_number "007"; gene_id "FBgn0023535"\n+X\tdexseq_prepare_annotation.py\texonic_part\t422062\t422067\t.\t+\t.\ttranscripts "FBtr0333318"; exonic_part_number "008"; gene_id "FBgn0023535"\n+X\tdexseq_prepare_annotation.py\taggregate_gene\t403545\t417259\t.\t-\t.\tgene_id "FBgn0260400"\n+X\tdexseq_prepare_annotation.py\texonic_part\t403545\t410882\t.\t-\t.\ttranscripts "FBtr0307173"; exonic_part_number "001"; gene_id "FBgn0260400"\n+X\tdexseq_prepare_annotation.py\texonic_part\t410883\t411268\t.\t-\t.\ttranscripts "FBtr0307173+FBtr0100254"; exonic_part_number "002"; gene_id "FBgn0260400"\n+X\tdexseq_prepare_annotation.py\texonic_part\t411269\t413275\t.\t-\t.\ttranscripts "FBtr0070091+FBtr0114366+FBtr0307173+FBtr0100254"; exonic_part_number "003"; gene_id "FBgn0260400"\n+X\tdexseq_prepare_annotation.py\texonic_part\t414110\t414315\t.\t-\t.\ttranscripts "FBtr0100254"; exonic_part_number "004"; gene_id "FBgn0260400"\n+X\tdexseq_prepare_annotation.py\texonic_part\t415473\t415729\t.\t-\t.\ttranscripts "FBtr0070091+FBtr0307173"; exonic_part_number "005"; gene_id "FBgn0260400"\n+X\tdexseq_prepare_annotation.py\texonic_part\t417019\t417259\t.\t-\t.\ttranscripts "FBtr0070091+FBtr0114366+FBtr0307173"; exonic_part_number "006"; gene_id "FBgn0260400"\n' |
| b |
| diff -r f89c9b25feb4 -r 251393b72616 test-data/original.gtf --- a/test-data/original.gtf Sat Jul 28 03:44:02 2018 -0400 +++ b/test-data/original.gtf Tue Dec 11 00:19:18 2018 -0500 |
| b |
| b'@@ -1,1000 +1,994 @@\n-dmel_mitochondrion_genome\ttRNA\texon\t1\t65\t.\t+\t.\tgene_id "FBgn0013696"; transcript_id "FBtr0100854"; exon_number "1"; gene_name "mt:tRNA:I"; gene_biotype "tRNA"; transcript_name "mt:tRNA:I-RA"; exon_id "FBgn0013696:1";\n-dmel_mitochondrion_genome\ttRNA\texon\t97\t165\t.\t-\t.\tgene_id "FBgn0013703"; transcript_id "FBtr0100855"; exon_number "1"; gene_name "mt:tRNA:Q"; gene_biotype "tRNA"; transcript_name "mt:tRNA:Q-RA"; exon_id "FBgn0013703:1";\n-dmel_mitochondrion_genome\ttRNA\texon\t171\t239\t.\t+\t.\tgene_id "FBgn0013700"; transcript_id "FBtr0100856"; exon_number "1"; gene_name "mt:tRNA:M"; gene_biotype "tRNA"; transcript_name "mt:tRNA:M-RA"; exon_id "FBgn0013700:1";\n-dmel_mitochondrion_genome\ttRNA\texon\t1322\t1383\t.\t-\t.\tgene_id "FBgn0013690"; transcript_id "FBtr0100859"; exon_number "1"; gene_name "mt:tRNA:C"; gene_biotype "tRNA"; transcript_name "mt:tRNA:C-RA"; exon_id "FBgn0013690:1";\n-dmel_mitochondrion_genome\ttRNA\texon\t1403\t1468\t.\t-\t.\tgene_id "FBgn0013710"; transcript_id "FBtr0100860"; exon_number "1"; gene_name "mt:tRNA:Y"; gene_biotype "tRNA"; transcript_name "mt:tRNA:Y-RA"; exon_id "FBgn0013710:1";\n-dmel_mitochondrion_genome\tprotein_coding\texon\t1474\t3009\t.\t+\t.\tgene_id "FBgn0013674"; transcript_id "FBtr0100861"; exon_number "1"; gene_name "mt:CoI"; gene_biotype "protein_coding"; transcript_name "mt:CoI-RA"; exon_id "FBgn0013674:1";\n-dmel_mitochondrion_genome\tprotein_coding\tCDS\t1474\t3006\t.\t+\t0\tgene_id "FBgn0013674"; transcript_id "FBtr0100861"; exon_number "1"; gene_name "mt:CoI"; gene_biotype "protein_coding"; transcript_name "mt:CoI-RA"; protein_id "FBpp0100176";\n-dmel_mitochondrion_genome\tprotein_coding\tstop_codon\t3007\t3009\t.\t+\t0\tgene_id "FBgn0013674"; transcript_id "FBtr0100861"; exon_number "1"; gene_name "mt:CoI"; gene_biotype "protein_coding"; transcript_name "mt:CoI-RA";\n-dmel_mitochondrion_genome\ttRNA\texon\t3012\t3077\t.\t+\t.\tgene_id "FBgn0013699"; transcript_id "FBtr0100862"; exon_number "1"; gene_name "mt:tRNA:L:UUR"; gene_biotype "tRNA"; transcript_name "mt:tRNA:L:UUR-RA"; exon_id "FBgn0013699:1";\n-dmel_mitochondrion_genome\tprotein_coding\texon\t3083\t3767\t.\t+\t.\tgene_id "FBgn0013675"; transcript_id "FBtr0100863"; exon_number "1"; gene_name "mt:CoII"; gene_biotype "protein_coding"; transcript_name "mt:CoII-RA"; exon_id "FBgn0013675:1";\n-dmel_mitochondrion_genome\tprotein_coding\tCDS\t3083\t3767\t.\t+\t0\tgene_id "FBgn0013675"; transcript_id "FBtr0100863"; exon_number "1"; gene_name "mt:CoII"; gene_biotype "protein_coding"; transcript_name "mt:CoII-RA"; protein_id "FBpp0100177";\n-dmel_mitochondrion_genome\tprotein_coding\tstart_codon\t3083\t3085\t.\t+\t0\tgene_id "FBgn0013675"; transcript_id "FBtr0100863"; exon_number "1"; gene_name "mt:CoII"; gene_biotype "protein_coding"; transcript_name "mt:CoII-RA";\n-dmel_mitochondrion_genome\ttRNA\texon\t3768\t3838\t.\t+\t.\tgene_id "FBgn0013697"; transcript_id "FBtr0100864"; exon_number "1"; gene_name "mt:tRNA:K"; gene_biotype "tRNA"; transcript_name "mt:tRNA:K-RA"; exon_id "FBgn0013697:1";\n-dmel_mitochondrion_genome\ttRNA\texon\t3840\t3906\t.\t+\t.\tgene_id "FBgn0013691"; transcript_id "FBtr0100865"; exon_number "1"; gene_name "mt:tRNA:D"; gene_biotype "tRNA"; transcript_name "mt:tRNA:D-RA"; exon_id "FBgn0013691:1";\n-dmel_mitochondrion_genome\ttRNA\texon\t5543\t5607\t.\t+\t.\tgene_id "FBgn0013694"; transcript_id "FBtr0100869"; exon_number "1"; gene_name "mt:tRNA:G"; gene_biotype "tRNA"; transcript_name "mt:tRNA:G-RA"; exon_id "FBgn0013694:1";\n-dmel_mitochondrion_genome\tprotein_coding\texon\t5608\t5961\t.\t+\t.\tgene_id "FBgn0013681"; transcript_id "FBtr0100870"; exon_number "1"; gene_name "mt:ND3"; gene_biotype "protein_coding"; transcript_name "mt:ND3-RA"; exon_id "FBgn0013681:1";\n-dmel_mitochondrion_genome\tprotein_coding\tCDS\t5608\t5958\t.\t+\t0\tgene_id "FBgn0013681"; transcript_id "FBtr0100870"; exon_number "1"; gene_name "mt:ND3"; gene_biotype "protein_coding"; transcript_name "mt:ND3-RA"; protein_id "FBpp0100181";\n-dmel_mitochondrion_genome\tprotein_coding\tstop_codon\t5959\t5961\t.\t+\t0\tgene_id "FBgn0013681"; transcript_id "F'..b'protein_coding"; transcript_name "elav-RD"; protein_id "FBpp0298002";\n+X\tprotein_coding\tstop_codon\t411825\t411827\t.\t-\t0\tgene_id "FBgn0260400"; transcript_id "FBtr0307173"; exon_number "3"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RD";\n+X\tprotein_coding\texon\t414110\t414315\t.\t-\t.\tgene_id "FBgn0260400"; transcript_id "FBtr0100254"; exon_number "1"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RB"; exon_id "FBgn0260400:4";\n+X\tprotein_coding\texon\t410883\t413275\t.\t-\t.\tgene_id "FBgn0260400"; transcript_id "FBtr0100254"; exon_number "2"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RB"; exon_id "FBgn0260400:2";\n+X\tprotein_coding\tCDS\t411828\t413264\t.\t-\t0\tgene_id "FBgn0260400"; transcript_id "FBtr0100254"; exon_number "2"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RB"; protein_id "FBpp0099643";\n+X\tprotein_coding\tstart_codon\t413262\t413264\t.\t-\t0\tgene_id "FBgn0260400"; transcript_id "FBtr0100254"; exon_number "2"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RB";\n+X\tprotein_coding\tstop_codon\t411825\t411827\t.\t-\t0\tgene_id "FBgn0260400"; transcript_id "FBtr0100254"; exon_number "2"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RB";\n+X\tprotein_coding\texon\t417019\t417259\t.\t-\t.\tgene_id "FBgn0260400"; transcript_id "FBtr0070091"; exon_number "1"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RA"; exon_id "FBgn0260400:6";\n+X\tprotein_coding\texon\t415473\t415729\t.\t-\t.\tgene_id "FBgn0260400"; transcript_id "FBtr0070091"; exon_number "2"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RA"; exon_id "FBgn0260400:5";\n+X\tprotein_coding\tCDS\t415473\t415473\t.\t-\t0\tgene_id "FBgn0260400"; transcript_id "FBtr0070091"; exon_number "2"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RA"; protein_id "FBpp0070086";\n+X\tprotein_coding\tstart_codon\t415473\t415473\t.\t-\t0\tgene_id "FBgn0260400"; transcript_id "FBtr0070091"; exon_number "2"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RA";\n+X\tprotein_coding\tstart_codon\t413274\t413275\t.\t-\t2\tgene_id "FBgn0260400"; transcript_id "FBtr0070091"; exon_number "3"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RA";\n+X\tprotein_coding\texon\t411269\t413275\t.\t-\t.\tgene_id "FBgn0260400"; transcript_id "FBtr0070091"; exon_number "3"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RA"; exon_id "FBgn0260400:3";\n+X\tprotein_coding\tCDS\t411828\t413275\t.\t-\t2\tgene_id "FBgn0260400"; transcript_id "FBtr0070091"; exon_number "3"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RA"; protein_id "FBpp0070086";\n+X\tprotein_coding\tstop_codon\t411825\t411827\t.\t-\t0\tgene_id "FBgn0260400"; transcript_id "FBtr0070091"; exon_number "3"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RA";\n+X\tprotein_coding\texon\t417019\t417259\t.\t-\t.\tgene_id "FBgn0260400"; transcript_id "FBtr0114366"; exon_number "1"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RC"; exon_id "FBgn0260400:6";\n+X\tprotein_coding\texon\t411269\t413275\t.\t-\t.\tgene_id "FBgn0260400"; transcript_id "FBtr0114366"; exon_number "2"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RC"; exon_id "FBgn0260400:344";\n+X\tprotein_coding\tCDS\t411828\t413264\t.\t-\t0\tgene_id "FBgn0260400"; transcript_id "FBtr0114366"; exon_number "2"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RC"; protein_id "FBpp0112915";\n+X\tprotein_coding\tstart_codon\t413262\t413264\t.\t-\t0\tgene_id "FBgn0260400"; transcript_id "FBtr0114366"; exon_number "2"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RC";\n+X\tprotein_coding\tstop_codon\t411825\t411827\t.\t-\t0\tgene_id "FBgn0260400"; transcript_id "FBtr0114366"; exon_number "2"; gene_name "elav"; gene_biotype "protein_coding"; transcript_name "elav-RC";\n\\ No newline at end of file\n' |
| b |
| diff -r f89c9b25feb4 -r 251393b72616 test-data/out_count.tab --- a/test-data/out_count.tab Sat Jul 28 03:44:02 2018 -0400 +++ b/test-data/out_count.tab Tue Dec 11 00:19:18 2018 -0500 |
| b |
| b'@@ -1,222 +1,244 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_ambiguous_readpair_position\t0\n-_empty\t0\n+_empty\t6206\n _lowaqual\t0\n _notaligned\t0\n' |