| Previous changeset 1:c80cdc2eac6d (2018-12-12) Next changeset 3:2bb86e2c417f (2019-05-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d |
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modified:
gffcompare.xml test-data/gffcompare_out1-1.tmap test-data/gffcompare_out1-2.tmap test-data/gffcompare_out1.gtf test-data/gffcompare_out1.stats test-data/gffcompare_out1.tracking test-data/gffcompare_out2.gtf test-data/gffcompare_out2.stats test-data/gffcompare_out2.tracking |
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| diff -r c80cdc2eac6d -r f99d7825a501 gffcompare.xml --- a/gffcompare.xml Wed Dec 12 03:19:14 2018 -0500 +++ b/gffcompare.xml Tue Feb 05 15:51:44 2019 -0500 |
| [ |
| @@ -1,16 +1,10 @@ -<tool id="gffcompare" name="GffCompare" version="0.9.8+galaxy1"> +<tool id="gffcompare" name="GffCompare" version="0.10.6"> <description>compare assembled transcripts to a reference annotation</description> <requirements> - <requirement type="package" version="0.9.8">gffcompare</requirement> + <requirement type="package" version="0.10.6">gffcompare</requirement> </requirements> - <stdio> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <regex match="Error" /> - <regex match="Exception" /> - </stdio> <version_command>gffcompare -v | awk '{print $2}'</version_command> - <command><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ #import re #set escaped_element_identifiers = [re.sub('[^\w\-]', '_', str(_.element_identifier)) for _ in $gffinputs] #for $input, $escaped_element_identifier in zip($gffinputs, $escaped_element_identifiers): @@ -43,11 +37,16 @@ $discard_single_exon -e $max_dist_exon -d $max_dist_group -$discard_intron_redundant_transfrags +-p '$adv_output.p' +$adv_output.A +$adv_output.C +$adv_output.X +$adv_output.K #for $escaped_element_identifier in $escaped_element_identifiers: '$escaped_element_identifier' #end for + ]]></command> <inputs> <param format="gtf" name="gffinputs" type="data" label="GTF inputs for comparison" help="" multiple="true" /> @@ -101,7 +100,13 @@ </param> <param argument="-e" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" label="Max. Distance for assessing exon accuracy" name="max_dist_exon" type="integer" value="100" /> <param argument="-d" help="max. distance (range) for grouping transcript start sites. Default: 100" label="Max distance for transcript grouping" name="max_dist_group" type="integer" value="100" /> - <param argument="-F" help="Discard intron-redundant transfrags if they share the 5' end (if they differ only at the 3' end)" truevalue="-F" falsevalue="" label="discard intron-redundant transfrags sharing 5'" name="discard_intron_redundant_transfrags" type="boolean" /> + <section name="adv_output" title="Options for the annotated/combined GTF output file"> + <param argument="-p" type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf (default: 'TCONS')" /> + <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue="" label="discard the 'contained' transfrags" help="i.e. collapse intron-redundant transfrags across all query files" /> + <param argument="-A" type="boolean" checked="false" truevalue="-A" falsevalue="" label="discard the 'contained' transfrags except intron-redundant transfrags starting with a different 5' exon" help="like -C but does not discard intron-redundant transfrags if they start with a different 5' exon" /> + <param argument="-X" type="boolean" checked="false" truevalue="-X" falsevalue="" label="discard the 'contained' transfrags also if ends stick out within the container's introns" help="like -C but also discard contained transfrags if transfrag ends stick out within the container's introns" /> + <param argument="-K" type="boolean" checked="false" truevalue="-A" falsevalue="" label="do NOT discard any redundant transfrag matching a reference" help="for -C/-A/-X" /> + </section> </inputs> <outputs> <data format="txt" from_work_dir="gffcmp.stats" label="${tool.name} on ${on_string}: transcript accuracy" name="transcripts_stats" /> @@ -135,7 +140,6 @@ <param name="discard_single_exon" value="" /> <param name="max_dist_exon" value="100" /> <param name="max_dist_group" value="100" /> - <param name="discard_intron_redundant_transfrags" value="No" /> <output file="gffcompare_out1.stats" name="transcripts_stats" lines_diff="6" /> <output file="gffcompare_out1.loci" name="transcripts_loci" lines_diff="2" /> <output file="gffcompare_out1.tracking" name="transcripts_tracking" /> @@ -162,7 +166,6 @@ <param name="discard_single_exon" value="" /> <param name="max_dist_exon" value="100" /> <param name="max_dist_group" value="100" /> - <param name="discard_intron_redundant_transfrags" value="No" /> <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" /> <output file="gffcompare_out2.loci" name="transcripts_loci" /> <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> @@ -183,7 +186,7 @@ (see manual: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/). Most of the options and parameters of CuffCompare are supported by GffCompare, while new features will likely be added to GffCompare in the future. -A notable difference from GffCompare is that when a single query GTF/GFF file is given as input, along with a reference annotation (-r option), +A notable difference of GffCompare is that when a single query GTF/GFF file is given as input, along with a reference annotation (-r option), gffcompare switches into "annotation mode" and it generates a .annotated.gtf file instead of the .merged.gtf produced by CuffCompare with the same parameters. This file has the same general format as CuffCompare's .merged.gtf file (with "class codes" assigned to transcripts as per their relationship with the matching/overlapping reference transcript), but the original transcript IDs are preserved, so gffcompare can thus |
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| diff -r c80cdc2eac6d -r f99d7825a501 test-data/gffcompare_out1-1.tmap --- a/test-data/gffcompare_out1-1.tmap Wed Dec 12 03:19:14 2018 -0500 +++ b/test-data/gffcompare_out1-1.tmap Tue Feb 05 15:51:44 2019 -0500 |
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| b'@@ -1,51 +1,51 @@\n-ref_gene_id\tref_id\tclass_code\tqry_gene_id\tqry_id\tFMI\tFPKM\tFPKM_conf_lo\tFPKM_conf_hi\tcov\tlen\tmajor_iso_id\tref_match_len\n--\t-\tu\tCUFF.1\tCUFF.1.1\t100\t20.607936\t0.000000\t49.751960\t1.317073\t41\tCUFF.1.1\t-\n--\t-\tu\tCUFF.3\tCUFF.3.1\t100\t27.255658\t0.000000\t65.800979\t1.741935\t31\tCUFF.3.1\t-\n--\t-\tu\tCUFF.5\tCUFF.5.1\t100\t31.293533\t0.000000\t75.549272\t2.000000\t27\tCUFF.5.1\t-\n--\t-\tu\tCUFF.7\tCUFF.7.1\t100\t9.999117\t0.000000\t19.998234\t0.639053\t169\tCUFF.7.1\t-\n--\t-\tu\tCUFF.9\tCUFF.9.1\t100\t17.776896\t9.153835\t26.399957\t1.136139\t404\tCUFF.9.1\t-\n--\t-\tu\tCUFF.11\tCUFF.11.1\t100\t31.293533\t0.000000\t75.549272\t2.000000\t27\tCUFF.11.1\t-\n-Xkr4\tXkr4\tc\tCUFF.13\tCUFF.13.1\t100\t10.695258\t0.000000\t25.820637\t0.683544\t79\tCUFF.13.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.15\tCUFF.15.1\t100\t10.695258\t0.000000\t25.820637\t0.683544\t79\tCUFF.15.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.17\tCUFF.17.1\t100\t8.710571\t0.000000\t21.029179\t0.556701\t97\tCUFF.17.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.19\tCUFF.19.1\t100\t29.337687\t3.097262\t55.578113\t1.875000\t72\tCUFF.19.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.21\tCUFF.21.1\t100\t13.851236\t0.000000\t33.439842\t0.885246\t61\tCUFF.21.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.23\tCUFF.23.1\t100\t23.470150\t0.000000\t50.571145\t1.500000\t54\tCUFF.23.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.25\tCUFF.25.1\t100\t14.567679\t5.354270\t23.781089\t0.931034\t290\tCUFF.25.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.27\tCUFF.27.1\t100\t34.253732\t0.000000\t73.806535\t2.189189\t37\tCUFF.27.1\t3634\n--\t-\tu\tCUFF.29\tCUFF.29.1\t100\t107.103219\t71.402146\t142.804292\t6.845070\t142\tCUFF.29.1\t-\n--\t-\tu\tCUFF.31\tCUFF.31.1\t100\t122.650461\t40.883487\t204.417435\t7.838710\t31\tCUFF.31.1\t-\n--\t-\tu\tCUFF.33\tCUFF.33.1\t100\t109.527366\t26.732460\t192.322273\t7.000000\t27\tCUFF.33.1\t-\n--\t-\tu\tCUFF.35\tCUFF.35.1\t100\t96.747183\t61.420107\t132.074259\t6.183206\t131\tCUFF.35.1\t-\n--\t-\tu\tCUFF.37\tCUFF.37.1\t100\t104.085013\t53.596365\t154.573660\t6.652174\t69\tCUFF.37.1\t-\n--\t-\tu\tCUFF.39\tCUFF.39.1\t100\t23.912983\t0.000000\t51.525317\t1.528302\t53\tCUFF.39.1\t-\n--\t-\tu\tCUFF.41\tCUFF.41.1\t100\t10.695258\t0.000000\t25.820637\t0.683544\t79\tCUFF.41.1\t-\n--\t-\tu\tCUFF.43\tCUFF.43.1\t100\t10.561567\t0.000000\t25.497879\t0.675000\t80\tCUFF.43.1\t-\n--\t-\tu\tCUFF.45\tCUFF.45.1\t100\t20.708956\t2.186303\t39.231609\t1.323529\t102\tCUFF.45.1\t-\n--\t-\tu\tCUFF.47\tCUFF.47.1\t100\t20.607936\t0.000000\t49.751960\t1.317073\t41\tCUFF.47.1\t-\n--\t-\tu\tCUFF.49\tCUFF.49.1\t100\t15.646767\t0.000000\t46.940300\t1.000000\t27\tCUFF.49.1\t-\n--\t-\tu\tCUFF.51\tCUFF.51.1\t100\t31.293533\t0.000000\t75.549272\t2.000000\t27\tCUFF.51.1\t-\n--\t-\tu\tCUFF.53\tCUFF.53.1\t100\t31.293533\t0.000000\t75.549272\t2.000000\t27\tCUFF.53.1\t-\n--\t-\tu\tCUFF.55\tCUFF.55.1\t100\t31.293533\t0.000000\t75.549272\t2.000000\t27\tCUFF.55.1\t-\n--\t-\tu\tCUFF.57\tCUFF.57.1\t100\t15.646767\t0.000000\t46.940300\t1.000000\t27\tCUFF.57.1\t-\n--\t-\tu\tCUFF.59\tCUFF.59.1\t100\t15.646767\t0.000000\t46.940300\t1.000000\t27\tCUFF.59.1\t-\n-Xkr4\tXkr4\ti\tCUFF.61\tCUFF.61.1\t100\t45.263860\t0.000000\t97.530065\t2.892857\t28\tCUFF.61.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.63\tCUFF.63.1\t100\t15.646767\t0.000000\t46.940300\t1.000000\t27\tCUFF.63.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.65\tCUFF.65.1\t100\t15.362280\t0.000000\t37.087825\t0.981818\t55\tCUFF.65.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.67\tCUFF.67.1\t100\t12.998852\t0.000000\t31.382005\t0.830769\t65\tCUFF.67.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.69\tCUFF.69.1\t100\t10.058636\t0.000000\t24.283695\t0.642857\t84\tCUFF.69.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.71\tCUFF.71.1\t100\t8.621688\t0.000000\t20.814595\t0.551020\t98\tCUFF.71.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.73\tCUFF.73.1\t100\t15.362280\t0.000000\t37.087825\t0.981818\t55\tCUFF.73.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.75\tCUFF.75.1\t100\t31.293533\t0.000000\t75.549272\t2.000000\t27\tCUFF.75.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.77\tCUFF.77.1\t100\t16.248565\t0.000000\t39.227507\t1.038462\t52\tCUFF.77.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.79\tCUFF.79.1\t100\t31.293533\t0.000000\t75.549272\t2.000000\t27\tCUFF.79.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.81\tCUFF.81.1\t100\t13.201959\t0.000000\t31.872349\t0.843750\t64\tCUFF.81.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.83\tCUFF.83.1\t100\t13.201959\t0.000000\t28.446269\t0.843750\t96\tCUFF.83.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.85\tCUFF.85.1\t100\t31.293533\t0.000000\t75.549272\t2.000000\t27\tCUFF.85.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.87\tCUFF.87.1\t100\t17.243375\t0.000000\t41.629191\t1.102041\t49\tCUFF.87.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.89\tCUFF.89.1\t100\t16.567165\t0.000000'..b'00\t21.481154\t0.000000\t46.285454\t1.372881\t59\tCUFF.97.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.99\tCUFF.99.1\t100\t14.567679\t0.000000\t35.169489\t0.931034\t58\tCUFF.99.1\t3634\n+ref_gene_id\tref_id\tclass_code\tqry_gene_id\tqry_id\tnum_exons\tFPKM\tTPM\t\tcov\tlen\tmajor_iso_id\tref_match_len\n+-\t-\tu\tCUFF.1\tCUFF.1.1\t1\t20.607936\t0.000000\t1.317073\t41\tCUFF.1.1\t-\n+-\t-\tu\tCUFF.3\tCUFF.3.1\t1\t27.255658\t0.000000\t1.741935\t31\tCUFF.3.1\t-\n+-\t-\tu\tCUFF.5\tCUFF.5.1\t1\t31.293533\t0.000000\t2.000000\t27\tCUFF.5.1\t-\n+-\t-\tu\tCUFF.7\tCUFF.7.1\t1\t9.999117\t0.000000\t0.639053\t169\tCUFF.7.1\t-\n+-\t-\tu\tCUFF.9\tCUFF.9.1\t1\t17.776896\t0.000000\t1.136139\t404\tCUFF.9.1\t-\n+-\t-\tu\tCUFF.11\tCUFF.11.1\t1\t31.293533\t0.000000\t2.000000\t27\tCUFF.11.1\t-\n+Xkr4\tXkr4\tc\tCUFF.13\tCUFF.13.1\t1\t10.695258\t0.000000\t0.683544\t79\tCUFF.13.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.15\tCUFF.15.1\t1\t10.695258\t0.000000\t0.683544\t79\tCUFF.15.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.17\tCUFF.17.1\t1\t8.710571\t0.000000\t0.556701\t97\tCUFF.17.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.19\tCUFF.19.1\t1\t29.337687\t0.000000\t1.875000\t72\tCUFF.19.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.21\tCUFF.21.1\t1\t13.851236\t0.000000\t0.885246\t61\tCUFF.21.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.23\tCUFF.23.1\t1\t23.470150\t0.000000\t1.500000\t54\tCUFF.23.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.25\tCUFF.25.1\t1\t14.567679\t0.000000\t0.931034\t290\tCUFF.25.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.27\tCUFF.27.1\t1\t34.253732\t0.000000\t2.189189\t37\tCUFF.27.1\t3634\n+-\t-\tu\tCUFF.29\tCUFF.29.1\t1\t107.103219\t0.000000\t6.845070\t142\tCUFF.29.1\t-\n+-\t-\tu\tCUFF.31\tCUFF.31.1\t1\t122.650461\t0.000000\t7.838710\t31\tCUFF.31.1\t-\n+-\t-\tu\tCUFF.33\tCUFF.33.1\t1\t109.527366\t0.000000\t7.000000\t27\tCUFF.33.1\t-\n+-\t-\tu\tCUFF.35\tCUFF.35.1\t1\t96.747183\t0.000000\t6.183206\t131\tCUFF.35.1\t-\n+-\t-\tu\tCUFF.37\tCUFF.37.1\t1\t104.085013\t0.000000\t6.652174\t69\tCUFF.37.1\t-\n+-\t-\tu\tCUFF.39\tCUFF.39.1\t1\t23.912983\t0.000000\t1.528302\t53\tCUFF.39.1\t-\n+-\t-\tu\tCUFF.41\tCUFF.41.1\t1\t10.695258\t0.000000\t0.683544\t79\tCUFF.41.1\t-\n+-\t-\tu\tCUFF.43\tCUFF.43.1\t1\t10.561567\t0.000000\t0.675000\t80\tCUFF.43.1\t-\n+-\t-\tu\tCUFF.45\tCUFF.45.1\t1\t20.708956\t0.000000\t1.323529\t102\tCUFF.45.1\t-\n+-\t-\tu\tCUFF.47\tCUFF.47.1\t1\t20.607936\t0.000000\t1.317073\t41\tCUFF.47.1\t-\n+-\t-\tu\tCUFF.49\tCUFF.49.1\t1\t15.646767\t0.000000\t1.000000\t27\tCUFF.49.1\t-\n+-\t-\tu\tCUFF.51\tCUFF.51.1\t1\t31.293533\t0.000000\t2.000000\t27\tCUFF.51.1\t-\n+-\t-\tu\tCUFF.53\tCUFF.53.1\t1\t31.293533\t0.000000\t2.000000\t27\tCUFF.53.1\t-\n+-\t-\tu\tCUFF.55\tCUFF.55.1\t1\t31.293533\t0.000000\t2.000000\t27\tCUFF.55.1\t-\n+-\t-\tu\tCUFF.57\tCUFF.57.1\t1\t15.646767\t0.000000\t1.000000\t27\tCUFF.57.1\t-\n+-\t-\tu\tCUFF.59\tCUFF.59.1\t1\t15.646767\t0.000000\t1.000000\t27\tCUFF.59.1\t-\n+Xkr4\tXkr4\ti\tCUFF.61\tCUFF.61.1\t1\t45.263860\t0.000000\t2.892857\t28\tCUFF.61.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.63\tCUFF.63.1\t1\t15.646767\t0.000000\t1.000000\t27\tCUFF.63.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.65\tCUFF.65.1\t1\t15.362280\t0.000000\t0.981818\t55\tCUFF.65.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.67\tCUFF.67.1\t1\t12.998852\t0.000000\t0.830769\t65\tCUFF.67.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.69\tCUFF.69.1\t1\t10.058636\t0.000000\t0.642857\t84\tCUFF.69.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.71\tCUFF.71.1\t1\t8.621688\t0.000000\t0.551020\t98\tCUFF.71.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.73\tCUFF.73.1\t1\t15.362280\t0.000000\t0.981818\t55\tCUFF.73.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.75\tCUFF.75.1\t1\t31.293533\t0.000000\t2.000000\t27\tCUFF.75.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.77\tCUFF.77.1\t1\t16.248565\t0.000000\t1.038462\t52\tCUFF.77.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.79\tCUFF.79.1\t1\t31.293533\t0.000000\t2.000000\t27\tCUFF.79.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.81\tCUFF.81.1\t1\t13.201959\t0.000000\t0.843750\t64\tCUFF.81.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.83\tCUFF.83.1\t1\t13.201959\t0.000000\t0.843750\t96\tCUFF.83.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.85\tCUFF.85.1\t1\t31.293533\t0.000000\t2.000000\t27\tCUFF.85.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.87\tCUFF.87.1\t1\t17.243375\t0.000000\t1.102041\t49\tCUFF.87.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.89\tCUFF.89.1\t1\t16.567165\t0.000000\t1.058824\t51\tCUFF.89.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.91\tCUFF.91.1\t1\t31.293533\t0.000000\t2.000000\t27\tCUFF.91.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.93\tCUFF.93.1\t1\t21.664754\t0.000000\t1.384615\t39\tCUFF.93.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.95\tCUFF.95.1\t1\t46.940300\t0.000000\t3.000000\t27\tCUFF.95.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.97\tCUFF.97.1\t1\t21.481154\t0.000000\t1.372881\t59\tCUFF.97.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.99\tCUFF.99.1\t1\t14.567679\t0.000000\t0.931034\t58\tCUFF.99.1\t3634\n' |
| b |
| diff -r c80cdc2eac6d -r f99d7825a501 test-data/gffcompare_out1-2.tmap --- a/test-data/gffcompare_out1-2.tmap Wed Dec 12 03:19:14 2018 -0500 +++ b/test-data/gffcompare_out1-2.tmap Tue Feb 05 15:51:44 2019 -0500 |
| b |
| b'@@ -1,51 +1,51 @@\n-ref_gene_id\tref_id\tclass_code\tqry_gene_id\tqry_id\tFMI\tFPKM\tFPKM_conf_lo\tFPKM_conf_hi\tcov\tlen\tmajor_iso_id\tref_match_len\n--\t-\tu\tCUFF.1\tCUFF.1.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.1.1\t-\n--\t-\tu\tCUFF.3\tCUFF.3.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.3.1\t-\n--\t-\tu\tCUFF.5\tCUFF.5.1\t100\t21.226627\t0.000000\t59.889707\t1.205672\t27\tCUFF.5.1\t-\n--\t-\tu\tCUFF.7\tCUFF.7.1\t100\t29.709524\t19.806349\t39.612698\t1.687500\t576\tCUFF.7.1\t-\n--\t-\tu\tCUFF.9\tCUFF.9.1\t100\t34.072933\t23.364686\t44.781179\t1.935341\t565\tCUFF.9.1\t-\n--\t-\tu\tCUFF.11\tCUFF.11.1\t100\t32.531777\t24.582998\t40.480555\t1.847804\t979\tCUFF.11.1\t-\n--\t-\tu\tCUFF.13\tCUFF.13.1\t100\t16.582060\t0.000000\t35.729373\t0.941860\t86\tCUFF.13.1\t-\n--\t-\tu\tCUFF.15\tCUFF.15.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.15.1\t-\n--\t-\tu\tCUFF.17\tCUFF.17.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.17.1\t-\n--\t-\tu\tCUFF.19\tCUFF.19.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.19.1\t-\n--\t-\tu\tCUFF.21\tCUFF.21.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.21.1\t-\n--\t-\tu\tCUFF.23\tCUFF.23.1\t100\t16.205195\t0.000000\t34.917342\t0.920455\t88\tCUFF.23.1\t-\n--\t-\tu\tCUFF.25\tCUFF.25.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.25.1\t-\n--\t-\tu\tCUFF.26\tCUFF.26.1\t100\t29.709524\t0.000000\t71.725135\t1.687500\t32\tCUFF.26.1\t-\n--\t-\tu\tCUFF.29\tCUFF.29.1\t100\t13.581496\t0.000000\t32.788633\t0.771429\t70\tCUFF.29.1\t-\n--\t-\tu\tCUFF.31\tCUFF.31.1\t100\t22.635827\t0.000000\t45.271655\t1.285714\t84\tCUFF.31.1\t-\n-Xkr4\tXkr4\ti\tCUFF.33\tCUFF.33.1\t100\t23.767619\t0.000000\t57.380108\t1.350000\t40\tCUFF.33.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.35\tCUFF.35.1\t100\t11.317914\t0.000000\t27.323861\t0.642857\t84\tCUFF.35.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.37\tCUFF.37.1\t100\t11.500461\t0.000000\t24.780049\t0.653226\t124\tCUFF.37.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.39\tCUFF.39.1\t100\t52.816931\t0.000000\t113.804669\t3.000000\t27\tCUFF.39.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.41\tCUFF.41.1\t100\t43.213852\t0.000000\t93.112911\t2.454545\t33\tCUFF.41.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.43\tCUFF.43.1\t100\t23.474191\t0.000000\t46.948383\t1.333333\t81\tCUFF.43.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.45\tCUFF.45.1\t100\t20.667495\t0.000000\t49.895746\t1.173913\t46\tCUFF.45.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.47\tCUFF.47.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.47.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.49\tCUFF.49.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.49.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.51\tCUFF.51.1\t100\t14.948188\t7.228977\t22.667399\t0.849057\t477\tCUFF.51.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.53\tCUFF.53.1\t100\t52.816931\t0.000000\t113.804669\t3.000000\t27\tCUFF.53.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.55\tCUFF.55.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.55.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.57\tCUFF.57.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.57.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.59\tCUFF.59.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.59.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.61\tCUFF.61.1\t100\t13.204233\t0.000000\t31.877838\t0.750000\t72\tCUFF.61.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.63\tCUFF.63.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.63.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.65\tCUFF.65.1\t100\t31.170648\t0.000000\t62.341295\t1.770492\t61\tCUFF.65.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.67\tCUFF.67.1\t100\t15.681351\t3.378764\t27.983938\t0.890700\t197\tCUFF.67.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.69\tCUFF.69.1\t100\t18.799247\t8.750627\t28.847866\t1.067797\t354\tCUFF.69.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.71\tCUFF.71.1\t100\t22.635827\t0.000000\t54.647722\t1.285714\t42\tCUFF.71.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.73\tCUFF.73.1\t100\t35.211287\t0.000000\t85.007567\t2.000000\t27\tCUFF.73.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.75\tCUFF.75.1\t100\t52.816931\t0.000000\t113.804669\t3.000000\t27\tCUFF.75.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.77\tCUFF.77.1\t100\t17.605644\t0.000000\t52.816931\t1.000000\t27\tCUFF.77.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.79\tCUFF.79.1\t100\t13.390208\t0.000000\t32.326821\t0.760563\t71\tCUFF.79.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.81\tCUFF.81.1\t100\t11.211141\t1.183592\t21.238690\t0.636792\t212\tCUFF.81.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.83\tCUFF.83.1\t100\t21.126772\t0.000000\t51.004540\t1.200000\t45\tCUFF.83.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.85\tCUFF.85.1\t100\t19.014095\t0.000000\t38.028190\t1.080000\t100\tCUFF.85.1\t3634\n-Xkr4\tXkr4\ti\tCUFF.87\tCUFF.87.1\t100\t24.170460\t0.000000\t52.080103\t1.372881\t59\tCUFF.87.1\t3634\n-'..b'34\n-Xkr4\tXkr4\ti\tCUFF.99\tCUFF.99.1\t100\t19.602160\t0.000000\t39.204320\t1.113402\t97\tCUFF.99.1\t3634\n+ref_gene_id\tref_id\tclass_code\tqry_gene_id\tqry_id\tnum_exons\tFPKM\tTPM\t\tcov\tlen\tmajor_iso_id\tref_match_len\n+-\t-\tu\tCUFF.1\tCUFF.1.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.1.1\t-\n+-\t-\tu\tCUFF.3\tCUFF.3.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.3.1\t-\n+-\t-\tu\tCUFF.5\tCUFF.5.1\t1\t21.226627\t0.000000\t1.205672\t27\tCUFF.5.1\t-\n+-\t-\tu\tCUFF.7\tCUFF.7.1\t1\t29.709524\t0.000000\t1.687500\t576\tCUFF.7.1\t-\n+-\t-\tu\tCUFF.9\tCUFF.9.1\t1\t34.072933\t0.000000\t1.935341\t565\tCUFF.9.1\t-\n+-\t-\tu\tCUFF.11\tCUFF.11.1\t1\t32.531777\t0.000000\t1.847804\t979\tCUFF.11.1\t-\n+-\t-\tu\tCUFF.13\tCUFF.13.1\t1\t16.582060\t0.000000\t0.941860\t86\tCUFF.13.1\t-\n+-\t-\tu\tCUFF.15\tCUFF.15.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.15.1\t-\n+-\t-\tu\tCUFF.17\tCUFF.17.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.17.1\t-\n+-\t-\tu\tCUFF.19\tCUFF.19.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.19.1\t-\n+-\t-\tu\tCUFF.21\tCUFF.21.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.21.1\t-\n+-\t-\tu\tCUFF.23\tCUFF.23.1\t1\t16.205195\t0.000000\t0.920455\t88\tCUFF.23.1\t-\n+-\t-\tu\tCUFF.25\tCUFF.25.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.25.1\t-\n+-\t-\tu\tCUFF.26\tCUFF.26.1\t1\t29.709524\t0.000000\t1.687500\t32\tCUFF.26.1\t-\n+-\t-\tu\tCUFF.29\tCUFF.29.1\t1\t13.581496\t0.000000\t0.771429\t70\tCUFF.29.1\t-\n+-\t-\tu\tCUFF.31\tCUFF.31.1\t1\t22.635827\t0.000000\t1.285714\t84\tCUFF.31.1\t-\n+Xkr4\tXkr4\ti\tCUFF.33\tCUFF.33.1\t1\t23.767619\t0.000000\t1.350000\t40\tCUFF.33.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.35\tCUFF.35.1\t1\t11.317914\t0.000000\t0.642857\t84\tCUFF.35.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.37\tCUFF.37.1\t1\t11.500461\t0.000000\t0.653226\t124\tCUFF.37.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.39\tCUFF.39.1\t1\t52.816931\t0.000000\t3.000000\t27\tCUFF.39.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.41\tCUFF.41.1\t1\t43.213852\t0.000000\t2.454545\t33\tCUFF.41.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.43\tCUFF.43.1\t1\t23.474191\t0.000000\t1.333333\t81\tCUFF.43.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.45\tCUFF.45.1\t1\t20.667495\t0.000000\t1.173913\t46\tCUFF.45.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.47\tCUFF.47.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.47.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.49\tCUFF.49.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.49.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.51\tCUFF.51.1\t1\t14.948188\t0.000000\t0.849057\t477\tCUFF.51.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.53\tCUFF.53.1\t1\t52.816931\t0.000000\t3.000000\t27\tCUFF.53.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.55\tCUFF.55.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.55.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.57\tCUFF.57.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.57.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.59\tCUFF.59.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.59.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.61\tCUFF.61.1\t1\t13.204233\t0.000000\t0.750000\t72\tCUFF.61.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.63\tCUFF.63.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.63.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.65\tCUFF.65.1\t1\t31.170648\t0.000000\t1.770492\t61\tCUFF.65.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.67\tCUFF.67.1\t1\t15.681351\t0.000000\t0.890700\t197\tCUFF.67.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.69\tCUFF.69.1\t1\t18.799247\t0.000000\t1.067797\t354\tCUFF.69.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.71\tCUFF.71.1\t1\t22.635827\t0.000000\t1.285714\t42\tCUFF.71.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.73\tCUFF.73.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.73.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.75\tCUFF.75.1\t1\t52.816931\t0.000000\t3.000000\t27\tCUFF.75.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.77\tCUFF.77.1\t1\t17.605644\t0.000000\t1.000000\t27\tCUFF.77.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.79\tCUFF.79.1\t1\t13.390208\t0.000000\t0.760563\t71\tCUFF.79.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.81\tCUFF.81.1\t1\t11.211141\t0.000000\t0.636792\t212\tCUFF.81.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.83\tCUFF.83.1\t1\t21.126772\t0.000000\t1.200000\t45\tCUFF.83.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.85\tCUFF.85.1\t1\t19.014095\t0.000000\t1.080000\t100\tCUFF.85.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.87\tCUFF.87.1\t1\t24.170460\t0.000000\t1.372881\t59\tCUFF.87.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.89\tCUFF.89.1\t1\t29.709524\t0.000000\t1.687500\t48\tCUFF.89.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.91\tCUFF.91.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.91.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.93\tCUFF.93.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.93.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.95\tCUFF.95.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.95.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.97\tCUFF.97.1\t1\t35.211287\t0.000000\t2.000000\t27\tCUFF.97.1\t3634\n+Xkr4\tXkr4\ti\tCUFF.99\tCUFF.99.1\t1\t19.602160\t0.000000\t1.113402\t97\tCUFF.99.1\t3634\n' |
| b |
| diff -r c80cdc2eac6d -r f99d7825a501 test-data/gffcompare_out1.gtf --- a/test-data/gffcompare_out1.gtf Wed Dec 12 03:19:14 2018 -0500 +++ b/test-data/gffcompare_out1.gtf Tue Feb 05 15:51:44 2019 -0500 |
| b |
| b'@@ -58,132 +58,136 @@\n chr1\tCufflinks\texon\t3197426\t3197452\t.\t.\t.\ttranscript_id "TCONS_00000060"; gene_id "XLOC_000024"; exon_number "1";\n chr1\tCufflinks\ttranscript\t3200023\t3200191\t.\t.\t.\ttranscript_id "TCONS_00000020"; gene_id "XLOC_000025"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS28";\n chr1\tCufflinks\texon\t3200023\t3200191\t.\t.\t.\ttranscript_id "TCONS_00000020"; gene_id "XLOC_000025"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3200057\t3200144\t.\t.\t.\ttranscript_id "TCONS_00000061"; gene_id "XLOC_000025"; oId "CUFF.23.1"; contained_in "TCONS_00000020"; class_code "u"; tss_id "TSS28";\n+chr1\tCufflinks\texon\t3200057\t3200144\t.\t.\t.\ttranscript_id "TCONS_00000061"; gene_id "XLOC_000025"; exon_number "1";\n chr1\tCufflinks\ttranscript\t3200326\t3200352\t.\t.\t.\ttranscript_id "TCONS_00000021"; gene_id "XLOC_000026"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29";\n chr1\tCufflinks\texon\t3200326\t3200352\t.\t.\t.\ttranscript_id "TCONS_00000021"; gene_id "XLOC_000026"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3200431\t3200457\t.\t.\t.\ttranscript_id "TCONS_00000061"; gene_id "XLOC_000027"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30";\n-chr1\tCufflinks\texon\t3200431\t3200457\t.\t.\t.\ttranscript_id "TCONS_00000061"; gene_id "XLOC_000027"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3201008\t3201039\t.\t.\t.\ttranscript_id "TCONS_00000062"; gene_id "XLOC_000028"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31";\n-chr1\tCufflinks\texon\t3201008\t3201039\t.\t.\t.\ttranscript_id "TCONS_00000062"; gene_id "XLOC_000028"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3200431\t3200457\t.\t.\t.\ttranscript_id "TCONS_00000062"; gene_id "XLOC_000027"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30";\n+chr1\tCufflinks\texon\t3200431\t3200457\t.\t.\t.\ttranscript_id "TCONS_00000062"; gene_id "XLOC_000027"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3201008\t3201039\t.\t.\t.\ttranscript_id "TCONS_00000063"; gene_id "XLOC_000028"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31";\n+chr1\tCufflinks\texon\t3201008\t3201039\t.\t.\t.\ttranscript_id "TCONS_00000063"; gene_id "XLOC_000028"; exon_number "1";\n chr1\tCufflinks\ttranscript\t3201078\t3201481\t.\t.\t.\ttranscript_id "TCONS_00000022"; gene_id "XLOC_000029"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS32";\n chr1\tCufflinks\texon\t3201078\t3201481\t.\t.\t.\ttranscript_id "TCONS_00000022"; gene_id "XLOC_000029"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3201597\t3201666\t.\t.\t.\ttranscript_id "TCONS_00000063"; gene_id "XLOC_000030"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33";\n-chr1\tCufflinks\texon\t3201597\t3201666\t.\t.\t.\ttranscript_id "TCONS_00000063"; gene_id "XLOC_000030"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3201161\t3201187\t.\t.\t.\ttranscript_id "TCONS_00000064"; gene_id "XLOC_000029"; oId "CUFF.25.1"; contained_in "TCONS_00000022"; class_code "u"; tss_id "TSS32";\n+chr1\tCufflinks\texon\t3201161\t3201187\t.\t.\t.\ttranscript_id "TCONS_00000064"; gene_id "XLOC_000029"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3201597\t3201666\t.\t.\t.\ttranscript_id "TCONS_00000065"; gene_id "XLOC_000030"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33";\n+chr1\tCufflinks\texon\t3201597\t3201666\t.\t.\t.\ttranscript_id "TCONS_00000065"; gene_id "XLOC_000030"; exon_number "1";\n chr1\tCufflinks\ttranscript\t3201673\t3201699\t.\t.\t.\ttranscript_id "TCONS_00000023"; gene_id "XLOC_000031"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34";\n chr1\tCufflinks\texon\t3201673\t3201699\t.\t.\t.\ttranscript_id "TCONS_00000023"; gene_id "XLOC_000031"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3201726\t3201809\t.\t.\t.\ttranscript_id "TCONS_00000064"; gene_id "XLOC_000032"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35";\n-chr1\tCufflinks\texon\t3201726\t3201809\t.\t.\t.\ttranscript_id "TCONS_00000064"; gene_id "XLOC_000032"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3211522\t3211561\t.\t.\t.\ttranscript_id "TCONS_00000065"; gene_id "XLOC_000033"; gene_name "Xkr4"; oId "CUFF.33.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS36";\n-chr1\tCufflinks\texon\t3211522\t3211561\t.\t.\t.\ttranscript_id "TCONS_00000065"; gene_id "XLOC_000033"; exon_number "1";\n+chr1\tCufflinks\tt'..b'"Xkr4"; oId "CUFF.91.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS82";\n-chr1\tCufflinks\texon\t3367211\t3367237\t.\t.\t.\ttranscript_id "TCONS_00000094"; gene_id "XLOC_000076"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3367211\t3367237\t.\t.\t.\ttranscript_id "TCONS_00000096"; gene_id "XLOC_000076"; gene_name "Xkr4"; oId "CUFF.91.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS82";\n+chr1\tCufflinks\texon\t3367211\t3367237\t.\t.\t.\ttranscript_id "TCONS_00000096"; gene_id "XLOC_000076"; exon_number "1";\n chr1\tCufflinks\ttranscript\t3367334\t3367382\t.\t.\t.\ttranscript_id "TCONS_00000044"; gene_id "XLOC_000077"; gene_name "Xkr4"; oId "CUFF.87.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS83";\n chr1\tCufflinks\texon\t3367334\t3367382\t.\t.\t.\ttranscript_id "TCONS_00000044"; gene_id "XLOC_000077"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3369581\t3369607\t.\t.\t.\ttranscript_id "TCONS_00000095"; gene_id "XLOC_000078"; gene_name "Xkr4"; oId "CUFF.93.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS84";\n-chr1\tCufflinks\texon\t3369581\t3369607\t.\t.\t.\ttranscript_id "TCONS_00000095"; gene_id "XLOC_000078"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3375002\t3375028\t.\t.\t.\ttranscript_id "TCONS_00000096"; gene_id "XLOC_000079"; gene_name "Xkr4"; oId "CUFF.95.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS85";\n-chr1\tCufflinks\texon\t3375002\t3375028\t.\t.\t.\ttranscript_id "TCONS_00000096"; gene_id "XLOC_000079"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3369581\t3369607\t.\t.\t.\ttranscript_id "TCONS_00000097"; gene_id "XLOC_000078"; gene_name "Xkr4"; oId "CUFF.93.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS84";\n+chr1\tCufflinks\texon\t3369581\t3369607\t.\t.\t.\ttranscript_id "TCONS_00000097"; gene_id "XLOC_000078"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3375002\t3375028\t.\t.\t.\ttranscript_id "TCONS_00000098"; gene_id "XLOC_000079"; gene_name "Xkr4"; oId "CUFF.95.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS85";\n+chr1\tCufflinks\texon\t3375002\t3375028\t.\t.\t.\ttranscript_id "TCONS_00000098"; gene_id "XLOC_000079"; exon_number "1";\n chr1\tCufflinks\ttranscript\t3377212\t3377262\t.\t.\t.\ttranscript_id "TCONS_00000045"; gene_id "XLOC_000080"; gene_name "Xkr4"; oId "CUFF.89.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS86";\n chr1\tCufflinks\texon\t3377212\t3377262\t.\t.\t.\ttranscript_id "TCONS_00000045"; gene_id "XLOC_000080"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3379889\t3379915\t.\t.\t.\ttranscript_id "TCONS_00000097"; gene_id "XLOC_000081"; gene_name "Xkr4"; oId "CUFF.97.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS87";\n-chr1\tCufflinks\texon\t3379889\t3379915\t.\t.\t.\ttranscript_id "TCONS_00000097"; gene_id "XLOC_000081"; exon_number "1";\n-chr1\tCufflinks\ttranscript\t3386740\t3386836\t.\t.\t.\ttranscript_id "TCONS_00000098"; gene_id "XLOC_000082"; gene_name "Xkr4"; oId "CUFF.99.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS88";\n-chr1\tCufflinks\texon\t3386740\t3386836\t.\t.\t.\ttranscript_id "TCONS_00000098"; gene_id "XLOC_000082"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3379889\t3379915\t.\t.\t.\ttranscript_id "TCONS_00000099"; gene_id "XLOC_000081"; gene_name "Xkr4"; oId "CUFF.97.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS87";\n+chr1\tCufflinks\texon\t3379889\t3379915\t.\t.\t.\ttranscript_id "TCONS_00000099"; gene_id "XLOC_000081"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3386740\t3386836\t.\t.\t.\ttranscript_id "TCONS_00000100"; gene_id "XLOC_000082"; gene_name "Xkr4"; oId "CUFF.99.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS88";\n+chr1\tCufflinks\texon\t3386740\t3386836\t.\t.\t.\ttranscript_id "TCONS_00000100"; gene_id "XLOC_000082"; exon_number "1";\n chr1\tCufflinks\ttranscript\t3391326\t3391352\t.\t.\t.\ttranscript_id "TCONS_00000046"; gene_id "XLOC_000083"; gene_name "Xkr4"; oId "CUFF.91.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS89";\n chr1\tCufflinks\texon\t3391326\t3391352\t.\t.\t.\ttranscript_id "TCONS_00000046"; gene_id "XLOC_000083"; exon_number "1";\n chr1\tCufflinks\ttranscript\t3435842\t3435880\t.\t.\t.\ttranscript_id "TCONS_00000047"; gene_id "XLOC_000084"; gene_name "Xkr4"; oId "CUFF.93.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS90";\n' |
| b |
| diff -r c80cdc2eac6d -r f99d7825a501 test-data/gffcompare_out1.stats --- a/test-data/gffcompare_out1.stats Wed Dec 12 03:19:14 2018 -0500 +++ b/test-data/gffcompare_out1.stats Tue Feb 05 15:51:44 2019 -0500 |
| b |
| @@ -1,8 +1,8 @@ -# gffcompare v0.9.8 | Command line was: -#gffcompare -r /tmp/tmp9HJ0Pt/files/000/dataset_364.dat -R -e 100 -d 100 /tmp/tmp9HJ0Pt/files/000/dataset_362.dat /tmp/tmp9HJ0Pt/files/000/dataset_363.dat +# gffcompare v0.10.6 | Command line was: +#gffcompare -r /tmp/tmp7AvPf0/files/000/dataset_3.dat -R -e 100 -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf # -#= Summary for dataset: /tmp/tmp9HJ0Pt/files/000/dataset_362.dat +#= Summary for dataset: gffcompare_in1_gtf # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) # (0 multi-transcript loci, ~1.0 transcripts per locus) # Reference mRNAs : 1 in 1 loci (1 multi-exon) @@ -25,10 +25,11 @@ Missed loci: 0/1 ( 0.0%) Novel loci: 49/50 ( 98.0%) -#= Summary for dataset: /tmp/tmp9HJ0Pt/files/000/dataset_363.dat +#= Summary for dataset: gffcompare_in2_gtf # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) # (0 multi-transcript loci, ~1.0 transcripts per locus) # Reference mRNAs : 0 in 0 loci (0 multi-exon) Total union super-loci across all input datasets: 87 (0 multi-transcript, ~1.1 transcripts per locus) +100 out of 100 consensus transcripts written in gffcmp.combined.gtf (0 discarded as redundant) |
| b |
| diff -r c80cdc2eac6d -r f99d7825a501 test-data/gffcompare_out1.tracking --- a/test-data/gffcompare_out1.tracking Wed Dec 12 03:19:14 2018 -0500 +++ b/test-data/gffcompare_out1.tracking Tue Feb 05 15:51:44 2019 -0500 |
| b |
| b'@@ -1,98 +1,100 @@\n-TCONS_00000001\tXLOC_000001\tXkr4|Xkr4\tc\tq1:CUFF.13|CUFF.13.1|100|10.695258|0.000000|25.820637|0.683544|-\t-\n-TCONS_00000002\tXLOC_000002\t-\tu\tq1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|-\t-\n-TCONS_00000003\tXLOC_000003\t-\tu\tq1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|-\t-\n-TCONS_00000004\tXLOC_000007\t-\tu\tq1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|-\t-\n-TCONS_00000005\tXLOC_000007\t-\tu\tq1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|-\t-\n-TCONS_00000006\tXLOC_000007\t-\tu\tq1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|-\t-\n-TCONS_00000007\tXLOC_000009\t-\tu\tq1:CUFF.35|CUFF.35.1|100|96.747183|61.420107|132.074259|6.183206|-\t-\n-TCONS_00000008\tXLOC_000009\t-\tu\tq1:CUFF.37|CUFF.37.1|100|104.085013|53.596365|154.573660|6.652174|-\t-\n-TCONS_00000009\tXLOC_000011\t-\tu\tq1:CUFF.39|CUFF.39.1|100|23.912983|0.000000|51.525317|1.528302|-\t-\n-TCONS_00000010\tXLOC_000012\t-\tu\tq1:CUFF.41|CUFF.41.1|100|10.695258|0.000000|25.820637|0.683544|-\t-\n-TCONS_00000011\tXLOC_000014\t-\tu\tq1:CUFF.43|CUFF.43.1|100|10.561567|0.000000|25.497879|0.675000|-\t-\n-TCONS_00000012\tXLOC_000015\t-\tu\tq1:CUFF.45|CUFF.45.1|100|20.708956|2.186303|39.231609|1.323529|-\t-\n-TCONS_00000013\tXLOC_000016\t-\tu\tq1:CUFF.47|CUFF.47.1|100|20.607936|0.000000|49.751960|1.317073|-\t-\n-TCONS_00000014\tXLOC_000017\t-\tu\tq1:CUFF.49|CUFF.49.1|100|15.646767|0.000000|46.940300|1.000000|-\t-\n-TCONS_00000015\tXLOC_000019\t-\tu\tq1:CUFF.51|CUFF.51.1|100|31.293533|0.000000|75.549272|2.000000|-\t-\n-TCONS_00000016\tXLOC_000020\t-\tu\tq1:CUFF.53|CUFF.53.1|100|31.293533|0.000000|75.549272|2.000000|-\t-\n-TCONS_00000017\tXLOC_000021\t-\tu\tq1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|-\t-\n-TCONS_00000018\tXLOC_000022\t-\tu\tq1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|-\t-\n-TCONS_00000019\tXLOC_000023\t-\tu\tq1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|-\t-\n-TCONS_00000020\tXLOC_000025\t-\tu\tq1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|169\tq2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|88\n-TCONS_00000021\tXLOC_000026\t-\tu\tq1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|-\t-\n-TCONS_00000022\tXLOC_000029\t-\tu\tq1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|404\tq2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|27\n-TCONS_00000023\tXLOC_000031\t-\tu\tq1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|-\t-\n-TCONS_00000024\tXLOC_000034\tXkr4|Xkr4\ti\tq1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|-\t-\n-TCONS_00000025\tXLOC_000035\tXkr4|Xkr4\ti\tq1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|-\t-\n-TCONS_00000026\tXLOC_000037\tXkr4|Xkr4\ti\tq1:CUFF.17|CUFF.17.1|100|8.710571|0.000000|21.029179|0.556701|-\t-\n-TCONS_00000027\tXLOC_000040\tXkr4|Xkr4\ti\tq1:CUFF.25|CUFF.25.1|100|14.567679|5.354270|23.781089|0.931034|-\t-\n-TCONS_00000028\tXLOC_000042\tXkr4|Xkr4\ti\tq1:CUFF.21|CUFF.21.1|100|13.851236|0.000000|33.439842|0.885246|-\t-\n-TCONS_00000029\tXLOC_000044\tXkr4|Xkr4\ti\tq1:CUFF.23|CUFF.23.1|100|23.470150|0.000000|50.571145|1.500000|-\t-\n-TCONS_00000030\tXLOC_000046\tXkr4|Xkr4\ti\tq1:CUFF.27|CUFF.27.1|100|34.253732|0.000000|73.806535|2.189189|-\t-\n-TCONS_00000031\tXLOC_000048\tXkr4|Xkr4\ti\tq1:CUFF.61|CUFF.61.1|100|45.263860|0.000000|97.530065|2.892857|-\t-\n-TCONS_00000032\tXLOC_000049\tXkr4|Xkr4\ti\tq1:CUFF.63|CUFF.63.1|100|15.646767|0.000000|46.940300|1.000000|-\t-\n-TCONS_00000033\tXLOC_000052\tXkr4|Xkr4\ti\tq1:CUFF.65|CUFF.65.1|100|15.362280|0.000000|37.087825|0.981818|-\t-\n-TCONS_00000034\tXLOC_000057\tXkr4|Xkr4\ti\tq1:CUFF.67|CUFF.67.1|100|12.998852|0.000000|31.382005|0.830769|-\t-\n-TCONS_00000035\tXLOC_000059\tXkr4|Xkr4\ti\tq1:CUFF.69|CUFF.69.1|100|10.058636|0.000000|24.283695|0.642857|-\t-\n-TCONS_00000036\tXLOC_000059\tXkr4|Xkr4\ti\tq1:CUFF.71|CUFF.71.1|100|8.621688|0.000000|20.814595|0.551020|-\t-\n-TCONS_00000037\tXLOC_000060\tXkr4|Xkr4\ti\tq1:CUFF.73|CUFF.73.1|100|15.362280|0.000000|37.087825|0.981818|-\t-\n-TCONS_00000038\tXLOC_000062\tXkr4|Xkr4\ti\tq1:CUFF.75|CUFF.75.1|100'..b'287|0.000000|2.000000|27\n+TCONS_00000059\tXLOC_000018\t-\tu\t-\tq2:CUFF.17|CUFF.17.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000060\tXLOC_000024\t-\tu\t-\tq2:CUFF.19|CUFF.19.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000061\tXLOC_000025\t-\tu\t-\tq2:CUFF.23|CUFF.23.1|1|16.205195|0.000000|0.920455|88\n+TCONS_00000062\tXLOC_000027\t-\tu\t-\tq2:CUFF.21|CUFF.21.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000063\tXLOC_000028\t-\tu\t-\tq2:CUFF.26|CUFF.26.1|1|29.709524|0.000000|1.687500|32\n+TCONS_00000064\tXLOC_000029\t-\tu\t-\tq2:CUFF.25|CUFF.25.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000065\tXLOC_000030\t-\tu\t-\tq2:CUFF.29|CUFF.29.1|1|13.581496|0.000000|0.771429|70\n+TCONS_00000066\tXLOC_000032\t-\tu\t-\tq2:CUFF.31|CUFF.31.1|1|22.635827|0.000000|1.285714|84\n+TCONS_00000067\tXLOC_000033\tXkr4|Xkr4\ti\t-\tq2:CUFF.33|CUFF.33.1|1|23.767619|0.000000|1.350000|40\n+TCONS_00000068\tXLOC_000036\tXkr4|Xkr4\ti\t-\tq2:CUFF.35|CUFF.35.1|1|11.317914|0.000000|0.642857|84\n+TCONS_00000069\tXLOC_000037\tXkr4|Xkr4\ti\t-\tq2:CUFF.37|CUFF.37.1|1|11.500461|0.000000|0.653226|124\n+TCONS_00000070\tXLOC_000038\tXkr4|Xkr4\ti\t-\tq2:CUFF.39|CUFF.39.1|1|52.816931|0.000000|3.000000|27\n+TCONS_00000071\tXLOC_000039\tXkr4|Xkr4\ti\t-\tq2:CUFF.41|CUFF.41.1|1|43.213852|0.000000|2.454545|33\n+TCONS_00000072\tXLOC_000041\tXkr4|Xkr4\ti\t-\tq2:CUFF.43|CUFF.43.1|1|23.474191|0.000000|1.333333|81\n+TCONS_00000073\tXLOC_000043\tXkr4|Xkr4\ti\t-\tq2:CUFF.45|CUFF.45.1|1|20.667495|0.000000|1.173913|46\n+TCONS_00000074\tXLOC_000045\tXkr4|Xkr4\ti\t-\tq2:CUFF.47|CUFF.47.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000075\tXLOC_000047\tXkr4|Xkr4\ti\t-\tq2:CUFF.49|CUFF.49.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000076\tXLOC_000049\tXkr4|Xkr4\ti\t-\tq2:CUFF.51|CUFF.51.1|1|14.948188|0.000000|0.849057|477\n+TCONS_00000077\tXLOC_000050\tXkr4|Xkr4\ti\t-\tq2:CUFF.53|CUFF.53.1|1|52.816931|0.000000|3.000000|27\n+TCONS_00000078\tXLOC_000051\tXkr4|Xkr4\ti\t-\tq2:CUFF.55|CUFF.55.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000079\tXLOC_000053\tXkr4|Xkr4\ti\t-\tq2:CUFF.57|CUFF.57.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000080\tXLOC_000054\tXkr4|Xkr4\ti\t-\tq2:CUFF.59|CUFF.59.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000081\tXLOC_000055\tXkr4|Xkr4\ti\t-\tq2:CUFF.61|CUFF.61.1|1|13.204233|0.000000|0.750000|72\n+TCONS_00000082\tXLOC_000056\tXkr4|Xkr4\ti\t-\tq2:CUFF.63|CUFF.63.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000083\tXLOC_000058\tXkr4|Xkr4\ti\t-\tq2:CUFF.65|CUFF.65.1|1|31.170648|0.000000|1.770492|61\n+TCONS_00000084\tXLOC_000059\tXkr4|Xkr4\ti\t-\tq2:CUFF.69|CUFF.69.1|1|18.799247|0.000000|1.067797|354\n+TCONS_00000085\tXLOC_000060\tXkr4|Xkr4\ti\t-\tq2:CUFF.67|CUFF.67.1|1|15.681351|0.000000|0.890700|197\n+TCONS_00000086\tXLOC_000061\tXkr4|Xkr4\ti\t-\tq2:CUFF.71|CUFF.71.1|1|22.635827|0.000000|1.285714|42\n+TCONS_00000087\tXLOC_000063\tXkr4|Xkr4\ti\t-\tq2:CUFF.73|CUFF.73.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000088\tXLOC_000064\tXkr4|Xkr4\ti\t-\tq2:CUFF.75|CUFF.75.1|1|52.816931|0.000000|3.000000|27\n+TCONS_00000089\tXLOC_000066\tXkr4|Xkr4\ti\t-\tq2:CUFF.77|CUFF.77.1|1|17.605644|0.000000|1.000000|27\n+TCONS_00000090\tXLOC_000067\tXkr4|Xkr4\ti\t-\tq2:CUFF.79|CUFF.79.1|1|13.390208|0.000000|0.760563|71\n+TCONS_00000091\tXLOC_000068\tXkr4|Xkr4\ti\t-\tq2:CUFF.81|CUFF.81.1|1|11.211141|0.000000|0.636792|212\n+TCONS_00000092\tXLOC_000069\tXkr4|Xkr4\ti\t-\tq2:CUFF.83|CUFF.83.1|1|21.126772|0.000000|1.200000|45\n+TCONS_00000093\tXLOC_000070\tXkr4|Xkr4\ti\t-\tq2:CUFF.85|CUFF.85.1|1|19.014095|0.000000|1.080000|100\n+TCONS_00000094\tXLOC_000072\tXkr4|Xkr4\ti\t-\tq2:CUFF.87|CUFF.87.1|1|24.170460|0.000000|1.372881|59\n+TCONS_00000095\tXLOC_000074\tXkr4|Xkr4\ti\t-\tq2:CUFF.89|CUFF.89.1|1|29.709524|0.000000|1.687500|48\n+TCONS_00000096\tXLOC_000076\tXkr4|Xkr4\ti\t-\tq2:CUFF.91|CUFF.91.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000097\tXLOC_000078\tXkr4|Xkr4\ti\t-\tq2:CUFF.93|CUFF.93.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000098\tXLOC_000079\tXkr4|Xkr4\ti\t-\tq2:CUFF.95|CUFF.95.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000099\tXLOC_000081\tXkr4|Xkr4\ti\t-\tq2:CUFF.97|CUFF.97.1|1|35.211287|0.000000|2.000000|27\n+TCONS_00000100\tXLOC_000082\tXkr4|Xkr4\ti\t-\tq2:CUFF.99|CUFF.99.1|1|19.602160|0.000000|1.113402|97\n' |
| b |
| diff -r c80cdc2eac6d -r f99d7825a501 test-data/gffcompare_out2.gtf --- a/test-data/gffcompare_out2.gtf Wed Dec 12 03:19:14 2018 -0500 +++ b/test-data/gffcompare_out2.gtf Tue Feb 05 15:51:44 2019 -0500 |
| b |
| @@ -126,7 +126,7 @@ chr1 StringTie exon 161082956 161083421 . + . transcript_id "MSTRG.21.1"; gene_id "MSTRG.21"; exon_number "1"; chr1 StringTie transcript 161084121 161084344 . + . transcript_id "MSTRG.22.1"; gene_id "MSTRG.22"; gene_name "uc007dfe.4"; xloc "XLOC_000009"; cmp_ref "uc007dfe.4"; class_code "c"; tss_id "TSS17"; chr1 StringTie exon 161084121 161084344 . + . transcript_id "MSTRG.22.1"; gene_id "MSTRG.22"; exon_number "1"; -chr1 StringTie transcript 161085014 161086329 . + . transcript_id "MSTRG.23.1"; gene_id "MSTRG.23"; gene_name "uc007dfe.4"; xloc "XLOC_000009"; cmp_ref "uc007dfe.4"; class_code "c"; tss_id "TSS18"; +chr1 StringTie transcript 161085014 161086329 . + . transcript_id "MSTRG.23.1"; gene_id "MSTRG.23"; gene_name "uc056yep.1"; xloc "XLOC_000009"; cmp_ref "uc056yep.1"; class_code "c"; tss_id "TSS18"; chr1 StringTie exon 161085014 161086329 . + . transcript_id "MSTRG.23.1"; gene_id "MSTRG.23"; exon_number "1"; chr1 StringTie transcript 161088497 161088913 . + . transcript_id "MSTRG.24.1"; gene_id "MSTRG.24"; gene_name "uc007dff.1"; xloc "XLOC_000010"; cmp_ref "uc007dff.1"; class_code "x"; tss_id "TSS19"; chr1 StringTie exon 161088497 161088913 . + . transcript_id "MSTRG.24.1"; gene_id "MSTRG.24"; exon_number "1"; |
| b |
| diff -r c80cdc2eac6d -r f99d7825a501 test-data/gffcompare_out2.stats --- a/test-data/gffcompare_out2.stats Wed Dec 12 03:19:14 2018 -0500 +++ b/test-data/gffcompare_out2.stats Tue Feb 05 15:51:44 2019 -0500 |
| b |
| @@ -1,14 +1,14 @@ -# gffcompare v0.9.8 | Command line was: -#gffcompare -r /tmp/tmp6wAQh6/files/000/dataset_668.dat -R -e 100 -d 100 /tmp/tmp6wAQh6/files/000/dataset_667.dat +# gffcompare v0.10.6 | Command line was: +#gffcompare -r /tmp/tmp7AvPf0/files/000/dataset_13.dat -R -T -e 100 -d 100 -p TCONS gffcompare_in4_gtf # -#= Summary for dataset: /tmp/tmp6wAQh6/files/000/dataset_667.dat +#= Summary for dataset: gffcompare_in4_gtf # Query mRNAs : 35 in 29 loci (15 multi-exon transcripts) # (3 multi-transcript loci, ~1.2 transcripts per locus) # Reference mRNAs : 20 in 7 loci (19 multi-exon) # Super-loci w/ reference transcripts: 6 #-----------------| Sensitivity | Precision | - Base level: 74.7 | 60.7 | + Base level: 72.6 | 60.7 | Exon level: 80.0 | 55.7 | Intron level: 81.2 | 64.4 | Intron chain level: 10.5 | 13.3 | @@ -27,3 +27,4 @@ Novel loci: 15/29 ( 51.7%) Total union super-loci across all input datasets: 21 +35 out of 35 consensus transcripts written in gffcmp.annotated.gtf (0 discarded as redundant) |
| b |
| diff -r c80cdc2eac6d -r f99d7825a501 test-data/gffcompare_out2.tracking --- a/test-data/gffcompare_out2.tracking Wed Dec 12 03:19:14 2018 -0500 +++ b/test-data/gffcompare_out2.tracking Tue Feb 05 15:51:44 2019 -0500 |
| b |
| @@ -1,35 +1,35 @@ -TCONS_00000001 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.3|MSTRG.3.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000002 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.4|MSTRG.4.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000003 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.5|MSTRG.5.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000004 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.6|MSTRG.6.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000005 XLOC_000002 - u q1:MSTRG.7|MSTRG.7.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000006 XLOC_000003 - u q1:MSTRG.10|MSTRG.10.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000007 XLOC_000004 - u q1:MSTRG.12|MSTRG.12.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000008 XLOC_000005 - u q1:MSTRG.13|MSTRG.13.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000009 XLOC_000006 uc007der.1|uc007der.1 x q1:MSTRG.14|MSTRG.14.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000010 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000011 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.2|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000012 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.3|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000013 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.4|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000014 XLOC_000007 uc007dev.1|uc007dev.1 = q1:MSTRG.16|MSTRG.16.5|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000015 XLOC_000008 uc007dey.2|uc007dey.2 s q1:MSTRG.18|MSTRG.18.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000016 XLOC_000008 uc007dey.2|uc007dey.2 s q1:MSTRG.18|MSTRG.18.2|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000017 XLOC_000009 uc007dfd.3|uc007dfd.3 c q1:MSTRG.20|MSTRG.20.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000018 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.21|MSTRG.21.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000019 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.22|MSTRG.22.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000020 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.23|MSTRG.23.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000021 XLOC_000010 uc007dff.1|uc007dff.1 x q1:MSTRG.24|MSTRG.24.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000022 XLOC_000011 uc007dff.1|uc007dff.1 s q1:MSTRG.26|MSTRG.26.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000023 XLOC_000012 uc007dff.1|uc007dff.1 i q1:MSTRG.28|MSTRG.28.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000024 XLOC_000013 - u q1:MSTRG.1|MSTRG.1.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000025 XLOC_000014 - u q1:MSTRG.2|MSTRG.2.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000026 XLOC_000015 - u q1:MSTRG.8|MSTRG.8.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000027 XLOC_000016 - u q1:MSTRG.9|MSTRG.9.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000028 XLOC_000017 - u q1:MSTRG.11|MSTRG.11.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000029 XLOC_000018 uc007des.1|uc007des.1 c q1:MSTRG.15|MSTRG.15.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000030 XLOC_000019 uc007dey.2|uc007dey.2 c q1:MSTRG.17|MSTRG.17.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000031 XLOC_000019 uc007dey.2|uc007dey.2 c q1:MSTRG.19|MSTRG.19.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000032 XLOC_000019 uc007dey.2|uc007dey.2 j q1:MSTRG.19|MSTRG.19.2|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000033 XLOC_000020 uc007dff.1|uc007dff.1 c q1:MSTRG.25|MSTRG.25.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000034 XLOC_000020 uc007dff.1|uc007dff.1 = q1:MSTRG.27|MSTRG.27.1|100|0.000000|0.000000|0.000000|0.000000|- -TCONS_00000035 XLOC_000021 - u q1:MSTRG.29|MSTRG.29.1|100|0.000000|0.000000|0.000000|0.000000|- +TCONS_00000001 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.3|MSTRG.3.1|3|0.000000|0.000000|0.000000|403 +TCONS_00000002 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.4|MSTRG.4.1|16|0.000000|0.000000|0.000000|3003 +TCONS_00000003 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.5|MSTRG.5.1|1|0.000000|0.000000|0.000000|3377 +TCONS_00000004 XLOC_000001 uc007del.2|uc007del.2 c q1:MSTRG.6|MSTRG.6.1|1|0.000000|0.000000|0.000000|2040 +TCONS_00000005 XLOC_000002 - u q1:MSTRG.7|MSTRG.7.1|1|0.000000|0.000000|0.000000|432 +TCONS_00000006 XLOC_000003 - u q1:MSTRG.10|MSTRG.10.1|1|0.000000|0.000000|0.000000|316 +TCONS_00000007 XLOC_000004 - u q1:MSTRG.12|MSTRG.12.1|1|0.000000|0.000000|0.000000|251 +TCONS_00000008 XLOC_000005 - u q1:MSTRG.13|MSTRG.13.1|1|0.000000|0.000000|0.000000|428 +TCONS_00000009 XLOC_000006 uc007der.1|uc007der.1 x q1:MSTRG.14|MSTRG.14.1|1|0.000000|0.000000|0.000000|250 +TCONS_00000010 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.1|11|0.000000|0.000000|0.000000|800 +TCONS_00000011 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.2|12|0.000000|0.000000|0.000000|608 +TCONS_00000012 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.3|11|0.000000|0.000000|0.000000|1008 +TCONS_00000013 XLOC_000007 uc007dev.1|uc007dev.1 j q1:MSTRG.16|MSTRG.16.4|11|0.000000|0.000000|0.000000|531 +TCONS_00000014 XLOC_000007 uc007dev.1|uc007dev.1 = q1:MSTRG.16|MSTRG.16.5|11|0.000000|0.000000|0.000000|807 +TCONS_00000015 XLOC_000008 uc007dey.2|uc007dey.2 s q1:MSTRG.18|MSTRG.18.1|16|0.000000|0.000000|0.000000|2459 +TCONS_00000016 XLOC_000008 uc007dey.2|uc007dey.2 s q1:MSTRG.18|MSTRG.18.2|6|0.000000|0.000000|0.000000|903 +TCONS_00000017 XLOC_000009 uc007dfd.3|uc007dfd.3 c q1:MSTRG.20|MSTRG.20.1|3|0.000000|0.000000|0.000000|716 +TCONS_00000018 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.21|MSTRG.21.1|1|0.000000|0.000000|0.000000|466 +TCONS_00000019 XLOC_000009 uc007dfe.4|uc007dfe.4 c q1:MSTRG.22|MSTRG.22.1|1|0.000000|0.000000|0.000000|224 +TCONS_00000020 XLOC_000009 uc056yep.1|uc056yep.1 c q1:MSTRG.23|MSTRG.23.1|1|0.000000|0.000000|0.000000|1316 +TCONS_00000021 XLOC_000010 uc007dff.1|uc007dff.1 x q1:MSTRG.24|MSTRG.24.1|1|0.000000|0.000000|0.000000|417 +TCONS_00000022 XLOC_000011 uc007dff.1|uc007dff.1 s q1:MSTRG.26|MSTRG.26.1|12|0.000000|0.000000|0.000000|3033 +TCONS_00000023 XLOC_000012 uc007dff.1|uc007dff.1 i q1:MSTRG.28|MSTRG.28.1|1|0.000000|0.000000|0.000000|213 +TCONS_00000024 XLOC_000013 - u q1:MSTRG.1|MSTRG.1.1|1|0.000000|0.000000|0.000000|447 +TCONS_00000025 XLOC_000014 - u q1:MSTRG.2|MSTRG.2.1|1|0.000000|0.000000|0.000000|349 +TCONS_00000026 XLOC_000015 - u q1:MSTRG.8|MSTRG.8.1|1|0.000000|0.000000|0.000000|1112 +TCONS_00000027 XLOC_000016 - u q1:MSTRG.9|MSTRG.9.1|1|0.000000|0.000000|0.000000|773 +TCONS_00000028 XLOC_000017 - u q1:MSTRG.11|MSTRG.11.1|1|0.000000|0.000000|0.000000|257 +TCONS_00000029 XLOC_000018 uc007des.1|uc007des.1 c q1:MSTRG.15|MSTRG.15.1|1|0.000000|0.000000|0.000000|353 +TCONS_00000030 XLOC_000019 uc007dey.2|uc007dey.2 c q1:MSTRG.17|MSTRG.17.1|6|0.000000|0.000000|0.000000|1029 +TCONS_00000031 XLOC_000019 uc007dey.2|uc007dey.2 c q1:MSTRG.19|MSTRG.19.1|11|0.000000|0.000000|0.000000|1514 +TCONS_00000032 XLOC_000019 uc007dey.2|uc007dey.2 j q1:MSTRG.19|MSTRG.19.2|10|0.000000|0.000000|0.000000|1478 +TCONS_00000033 XLOC_000020 uc007dff.1|uc007dff.1 c q1:MSTRG.25|MSTRG.25.1|1|0.000000|0.000000|0.000000|1361 +TCONS_00000034 XLOC_000020 uc007dff.1|uc007dff.1 = q1:MSTRG.27|MSTRG.27.1|12|0.000000|0.000000|0.000000|2016 +TCONS_00000035 XLOC_000021 - u q1:MSTRG.29|MSTRG.29.1|1|0.000000|0.000000|0.000000|223 |