Mercurial > repos > iuc > gffcompare
changeset 2:f99d7825a501 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit a5352fb7f073b0083b750c5cf7d283ebcc16b30d
| author | iuc |
|---|---|
| date | Tue, 05 Feb 2019 15:51:44 -0500 |
| parents | c80cdc2eac6d |
| children | 2bb86e2c417f |
| files | 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 |
| diffstat | 9 files changed, 348 insertions(+), 337 deletions(-) [+] |
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--- 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
--- 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 @@ -1,51 +1,51 @@ -ref_gene_id ref_id class_code qry_gene_id qry_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 - -Xkr4 Xkr4 c CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 3634 -Xkr4 Xkr4 i CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 3634 -Xkr4 Xkr4 i CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 3634 -Xkr4 Xkr4 i CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 3634 -Xkr4 Xkr4 i CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 3634 -Xkr4 Xkr4 i CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 3634 -Xkr4 Xkr4 i CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 3634 -Xkr4 Xkr4 i CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 3634 -- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 - -- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 - -- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 - -- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 - -- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 - -- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 - -- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 - -- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 - -- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 - -- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 - -- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 - -- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 - -- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 - -- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 - -- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 - -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 3634 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 3634 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 3634 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 3634 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 3634 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 3634 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 3634 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 3634 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 3634 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 3634 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 3634 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 3634 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 3634 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 3634 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 3634 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 3634 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 3634 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 3634 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 3634 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 3634 +ref_gene_id ref_id class_code qry_gene_id qry_id num_exons FPKM TPM cov len major_iso_id ref_match_len +- - u CUFF.1 CUFF.1.1 1 20.607936 0.000000 1.317073 41 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 1 27.255658 0.000000 1.741935 31 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 1 31.293533 0.000000 2.000000 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 1 9.999117 0.000000 0.639053 169 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 1 17.776896 0.000000 1.136139 404 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 1 31.293533 0.000000 2.000000 27 CUFF.11.1 - +Xkr4 Xkr4 c CUFF.13 CUFF.13.1 1 10.695258 0.000000 0.683544 79 CUFF.13.1 3634 +Xkr4 Xkr4 i CUFF.15 CUFF.15.1 1 10.695258 0.000000 0.683544 79 CUFF.15.1 3634 +Xkr4 Xkr4 i CUFF.17 CUFF.17.1 1 8.710571 0.000000 0.556701 97 CUFF.17.1 3634 +Xkr4 Xkr4 i CUFF.19 CUFF.19.1 1 29.337687 0.000000 1.875000 72 CUFF.19.1 3634 +Xkr4 Xkr4 i CUFF.21 CUFF.21.1 1 13.851236 0.000000 0.885246 61 CUFF.21.1 3634 +Xkr4 Xkr4 i CUFF.23 CUFF.23.1 1 23.470150 0.000000 1.500000 54 CUFF.23.1 3634 +Xkr4 Xkr4 i CUFF.25 CUFF.25.1 1 14.567679 0.000000 0.931034 290 CUFF.25.1 3634 +Xkr4 Xkr4 i CUFF.27 CUFF.27.1 1 34.253732 0.000000 2.189189 37 CUFF.27.1 3634 +- - u CUFF.29 CUFF.29.1 1 107.103219 0.000000 6.845070 142 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 1 122.650461 0.000000 7.838710 31 CUFF.31.1 - +- - u CUFF.33 CUFF.33.1 1 109.527366 0.000000 7.000000 27 CUFF.33.1 - +- - u CUFF.35 CUFF.35.1 1 96.747183 0.000000 6.183206 131 CUFF.35.1 - +- - u CUFF.37 CUFF.37.1 1 104.085013 0.000000 6.652174 69 CUFF.37.1 - +- - u CUFF.39 CUFF.39.1 1 23.912983 0.000000 1.528302 53 CUFF.39.1 - +- - u CUFF.41 CUFF.41.1 1 10.695258 0.000000 0.683544 79 CUFF.41.1 - +- - u CUFF.43 CUFF.43.1 1 10.561567 0.000000 0.675000 80 CUFF.43.1 - +- - u CUFF.45 CUFF.45.1 1 20.708956 0.000000 1.323529 102 CUFF.45.1 - +- - u CUFF.47 CUFF.47.1 1 20.607936 0.000000 1.317073 41 CUFF.47.1 - +- - u CUFF.49 CUFF.49.1 1 15.646767 0.000000 1.000000 27 CUFF.49.1 - +- - u CUFF.51 CUFF.51.1 1 31.293533 0.000000 2.000000 27 CUFF.51.1 - +- - u CUFF.53 CUFF.53.1 1 31.293533 0.000000 2.000000 27 CUFF.53.1 - +- - u CUFF.55 CUFF.55.1 1 31.293533 0.000000 2.000000 27 CUFF.55.1 - +- - u CUFF.57 CUFF.57.1 1 15.646767 0.000000 1.000000 27 CUFF.57.1 - +- - u CUFF.59 CUFF.59.1 1 15.646767 0.000000 1.000000 27 CUFF.59.1 - +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 1 45.263860 0.000000 2.892857 28 CUFF.61.1 3634 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 1 15.646767 0.000000 1.000000 27 CUFF.63.1 3634 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 1 15.362280 0.000000 0.981818 55 CUFF.65.1 3634 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 1 12.998852 0.000000 0.830769 65 CUFF.67.1 3634 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 1 10.058636 0.000000 0.642857 84 CUFF.69.1 3634 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 1 8.621688 0.000000 0.551020 98 CUFF.71.1 3634 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 1 15.362280 0.000000 0.981818 55 CUFF.73.1 3634 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 1 31.293533 0.000000 2.000000 27 CUFF.75.1 3634 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 1 16.248565 0.000000 1.038462 52 CUFF.77.1 3634 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 1 31.293533 0.000000 2.000000 27 CUFF.79.1 3634 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 1 13.201959 0.000000 0.843750 64 CUFF.81.1 3634 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 1 13.201959 0.000000 0.843750 96 CUFF.83.1 3634 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 1 31.293533 0.000000 2.000000 27 CUFF.85.1 3634 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 1 17.243375 0.000000 1.102041 49 CUFF.87.1 3634 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 1 16.567165 0.000000 1.058824 51 CUFF.89.1 3634 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 1 31.293533 0.000000 2.000000 27 CUFF.91.1 3634 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 1 21.664754 0.000000 1.384615 39 CUFF.93.1 3634 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 1 46.940300 0.000000 3.000000 27 CUFF.95.1 3634 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 1 21.481154 0.000000 1.372881 59 CUFF.97.1 3634 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 1 14.567679 0.000000 0.931034 58 CUFF.99.1 3634
--- 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 @@ -1,51 +1,51 @@ -ref_gene_id ref_id class_code qry_gene_id qry_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 - -- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 - -- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 - -- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 - -- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 - -- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 - -- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 - -- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 - -- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 - -- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 - -Xkr4 Xkr4 i CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 3634 -Xkr4 Xkr4 i CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 3634 -Xkr4 Xkr4 i CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 3634 -Xkr4 Xkr4 i CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 3634 -Xkr4 Xkr4 i CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 3634 -Xkr4 Xkr4 i CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 3634 -Xkr4 Xkr4 i CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 3634 -Xkr4 Xkr4 i CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 3634 -Xkr4 Xkr4 i CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 3634 -Xkr4 Xkr4 i CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 3634 -Xkr4 Xkr4 i CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 3634 -Xkr4 Xkr4 i CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 3634 -Xkr4 Xkr4 i CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 3634 -Xkr4 Xkr4 i CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 3634 -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 3634 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 3634 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 3634 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 3634 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 3634 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 3634 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 3634 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 3634 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 3634 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 3634 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 3634 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 3634 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 3634 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 3634 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 3634 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 3634 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 3634 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 3634 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 3634 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 3634 +ref_gene_id ref_id class_code qry_gene_id qry_id num_exons FPKM TPM cov len major_iso_id ref_match_len +- - u CUFF.1 CUFF.1.1 1 35.211287 0.000000 2.000000 27 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 1 35.211287 0.000000 2.000000 27 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 1 21.226627 0.000000 1.205672 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 1 29.709524 0.000000 1.687500 576 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 1 34.072933 0.000000 1.935341 565 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 1 32.531777 0.000000 1.847804 979 CUFF.11.1 - +- - u CUFF.13 CUFF.13.1 1 16.582060 0.000000 0.941860 86 CUFF.13.1 - +- - u CUFF.15 CUFF.15.1 1 35.211287 0.000000 2.000000 27 CUFF.15.1 - +- - u CUFF.17 CUFF.17.1 1 35.211287 0.000000 2.000000 27 CUFF.17.1 - +- - u CUFF.19 CUFF.19.1 1 35.211287 0.000000 2.000000 27 CUFF.19.1 - +- - u CUFF.21 CUFF.21.1 1 35.211287 0.000000 2.000000 27 CUFF.21.1 - +- - u CUFF.23 CUFF.23.1 1 16.205195 0.000000 0.920455 88 CUFF.23.1 - +- - u CUFF.25 CUFF.25.1 1 35.211287 0.000000 2.000000 27 CUFF.25.1 - +- - u CUFF.26 CUFF.26.1 1 29.709524 0.000000 1.687500 32 CUFF.26.1 - +- - u CUFF.29 CUFF.29.1 1 13.581496 0.000000 0.771429 70 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 1 22.635827 0.000000 1.285714 84 CUFF.31.1 - +Xkr4 Xkr4 i CUFF.33 CUFF.33.1 1 23.767619 0.000000 1.350000 40 CUFF.33.1 3634 +Xkr4 Xkr4 i CUFF.35 CUFF.35.1 1 11.317914 0.000000 0.642857 84 CUFF.35.1 3634 +Xkr4 Xkr4 i CUFF.37 CUFF.37.1 1 11.500461 0.000000 0.653226 124 CUFF.37.1 3634 +Xkr4 Xkr4 i CUFF.39 CUFF.39.1 1 52.816931 0.000000 3.000000 27 CUFF.39.1 3634 +Xkr4 Xkr4 i CUFF.41 CUFF.41.1 1 43.213852 0.000000 2.454545 33 CUFF.41.1 3634 +Xkr4 Xkr4 i CUFF.43 CUFF.43.1 1 23.474191 0.000000 1.333333 81 CUFF.43.1 3634 +Xkr4 Xkr4 i CUFF.45 CUFF.45.1 1 20.667495 0.000000 1.173913 46 CUFF.45.1 3634 +Xkr4 Xkr4 i CUFF.47 CUFF.47.1 1 35.211287 0.000000 2.000000 27 CUFF.47.1 3634 +Xkr4 Xkr4 i CUFF.49 CUFF.49.1 1 35.211287 0.000000 2.000000 27 CUFF.49.1 3634 +Xkr4 Xkr4 i CUFF.51 CUFF.51.1 1 14.948188 0.000000 0.849057 477 CUFF.51.1 3634 +Xkr4 Xkr4 i CUFF.53 CUFF.53.1 1 52.816931 0.000000 3.000000 27 CUFF.53.1 3634 +Xkr4 Xkr4 i CUFF.55 CUFF.55.1 1 35.211287 0.000000 2.000000 27 CUFF.55.1 3634 +Xkr4 Xkr4 i CUFF.57 CUFF.57.1 1 35.211287 0.000000 2.000000 27 CUFF.57.1 3634 +Xkr4 Xkr4 i CUFF.59 CUFF.59.1 1 35.211287 0.000000 2.000000 27 CUFF.59.1 3634 +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 1 13.204233 0.000000 0.750000 72 CUFF.61.1 3634 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 1 35.211287 0.000000 2.000000 27 CUFF.63.1 3634 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 1 31.170648 0.000000 1.770492 61 CUFF.65.1 3634 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 1 15.681351 0.000000 0.890700 197 CUFF.67.1 3634 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 1 18.799247 0.000000 1.067797 354 CUFF.69.1 3634 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 1 22.635827 0.000000 1.285714 42 CUFF.71.1 3634 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 1 35.211287 0.000000 2.000000 27 CUFF.73.1 3634 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 1 52.816931 0.000000 3.000000 27 CUFF.75.1 3634 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 1 17.605644 0.000000 1.000000 27 CUFF.77.1 3634 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 1 13.390208 0.000000 0.760563 71 CUFF.79.1 3634 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 1 11.211141 0.000000 0.636792 212 CUFF.81.1 3634 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 1 21.126772 0.000000 1.200000 45 CUFF.83.1 3634 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 1 19.014095 0.000000 1.080000 100 CUFF.85.1 3634 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 1 24.170460 0.000000 1.372881 59 CUFF.87.1 3634 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 1 29.709524 0.000000 1.687500 48 CUFF.89.1 3634 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 1 35.211287 0.000000 2.000000 27 CUFF.91.1 3634 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 1 35.211287 0.000000 2.000000 27 CUFF.93.1 3634 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 1 35.211287 0.000000 2.000000 27 CUFF.95.1 3634 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 1 35.211287 0.000000 2.000000 27 CUFF.97.1 3634 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 1 19.602160 0.000000 1.113402 97 CUFF.99.1 3634
--- 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 @@ -58,132 +58,136 @@ chr1 Cufflinks exon 3197426 3197452 . . . transcript_id "TCONS_00000060"; gene_id "XLOC_000024"; exon_number "1"; chr1 Cufflinks transcript 3200023 3200191 . . . transcript_id "TCONS_00000020"; gene_id "XLOC_000025"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS28"; chr1 Cufflinks exon 3200023 3200191 . . . transcript_id "TCONS_00000020"; gene_id "XLOC_000025"; exon_number "1"; +chr1 Cufflinks transcript 3200057 3200144 . . . transcript_id "TCONS_00000061"; gene_id "XLOC_000025"; oId "CUFF.23.1"; contained_in "TCONS_00000020"; class_code "u"; tss_id "TSS28"; +chr1 Cufflinks exon 3200057 3200144 . . . transcript_id "TCONS_00000061"; gene_id "XLOC_000025"; exon_number "1"; chr1 Cufflinks transcript 3200326 3200352 . . . transcript_id "TCONS_00000021"; gene_id "XLOC_000026"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29"; chr1 Cufflinks exon 3200326 3200352 . . . transcript_id "TCONS_00000021"; gene_id "XLOC_000026"; exon_number "1"; -chr1 Cufflinks transcript 3200431 3200457 . . . transcript_id "TCONS_00000061"; gene_id "XLOC_000027"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30"; -chr1 Cufflinks exon 3200431 3200457 . . . transcript_id "TCONS_00000061"; gene_id "XLOC_000027"; exon_number "1"; -chr1 Cufflinks transcript 3201008 3201039 . . . transcript_id "TCONS_00000062"; gene_id "XLOC_000028"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31"; -chr1 Cufflinks exon 3201008 3201039 . . . transcript_id "TCONS_00000062"; gene_id "XLOC_000028"; exon_number "1"; +chr1 Cufflinks transcript 3200431 3200457 . . . transcript_id "TCONS_00000062"; gene_id "XLOC_000027"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30"; +chr1 Cufflinks exon 3200431 3200457 . . . transcript_id "TCONS_00000062"; gene_id "XLOC_000027"; exon_number "1"; +chr1 Cufflinks transcript 3201008 3201039 . . . transcript_id "TCONS_00000063"; gene_id "XLOC_000028"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31"; +chr1 Cufflinks exon 3201008 3201039 . . . transcript_id "TCONS_00000063"; gene_id "XLOC_000028"; exon_number "1"; chr1 Cufflinks transcript 3201078 3201481 . . . transcript_id "TCONS_00000022"; gene_id "XLOC_000029"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS32"; chr1 Cufflinks exon 3201078 3201481 . . . transcript_id "TCONS_00000022"; gene_id "XLOC_000029"; exon_number "1"; -chr1 Cufflinks transcript 3201597 3201666 . . . transcript_id "TCONS_00000063"; gene_id "XLOC_000030"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33"; -chr1 Cufflinks exon 3201597 3201666 . . . transcript_id "TCONS_00000063"; gene_id "XLOC_000030"; exon_number "1"; +chr1 Cufflinks transcript 3201161 3201187 . . . transcript_id "TCONS_00000064"; gene_id "XLOC_000029"; oId "CUFF.25.1"; contained_in "TCONS_00000022"; class_code "u"; tss_id "TSS32"; +chr1 Cufflinks exon 3201161 3201187 . . . transcript_id "TCONS_00000064"; gene_id "XLOC_000029"; exon_number "1"; +chr1 Cufflinks transcript 3201597 3201666 . . . transcript_id "TCONS_00000065"; gene_id "XLOC_000030"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33"; +chr1 Cufflinks exon 3201597 3201666 . . . transcript_id "TCONS_00000065"; gene_id "XLOC_000030"; exon_number "1"; chr1 Cufflinks transcript 3201673 3201699 . . . transcript_id "TCONS_00000023"; gene_id "XLOC_000031"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34"; chr1 Cufflinks exon 3201673 3201699 . . . transcript_id "TCONS_00000023"; gene_id "XLOC_000031"; exon_number "1"; -chr1 Cufflinks transcript 3201726 3201809 . . . transcript_id "TCONS_00000064"; gene_id "XLOC_000032"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35"; -chr1 Cufflinks exon 3201726 3201809 . . . transcript_id "TCONS_00000064"; gene_id "XLOC_000032"; exon_number "1"; -chr1 Cufflinks transcript 3211522 3211561 . . . transcript_id "TCONS_00000065"; gene_id "XLOC_000033"; gene_name "Xkr4"; oId "CUFF.33.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS36"; -chr1 Cufflinks exon 3211522 3211561 . . . transcript_id "TCONS_00000065"; gene_id "XLOC_000033"; exon_number "1"; +chr1 Cufflinks transcript 3201726 3201809 . . . transcript_id "TCONS_00000066"; gene_id "XLOC_000032"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35"; +chr1 Cufflinks exon 3201726 3201809 . . . transcript_id "TCONS_00000066"; gene_id "XLOC_000032"; exon_number "1"; +chr1 Cufflinks transcript 3211522 3211561 . . . transcript_id "TCONS_00000067"; gene_id "XLOC_000033"; gene_name "Xkr4"; oId "CUFF.33.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS36"; +chr1 Cufflinks exon 3211522 3211561 . . . transcript_id "TCONS_00000067"; gene_id "XLOC_000033"; exon_number "1"; chr1 Cufflinks transcript 3212214 3212292 . . . transcript_id "TCONS_00000024"; gene_id "XLOC_000034"; gene_name "Xkr4"; oId "CUFF.15.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS37"; chr1 Cufflinks exon 3212214 3212292 . . . transcript_id "TCONS_00000024"; gene_id "XLOC_000034"; exon_number "1"; chr1 Cufflinks transcript 3212368 3212439 . . . transcript_id "TCONS_00000025"; gene_id "XLOC_000035"; gene_name "Xkr4"; oId "CUFF.19.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS38"; chr1 Cufflinks exon 3212368 3212439 . . . transcript_id "TCONS_00000025"; gene_id "XLOC_000035"; exon_number "1"; -chr1 Cufflinks transcript 3212718 3212801 . . . transcript_id "TCONS_00000066"; gene_id "XLOC_000036"; gene_name "Xkr4"; oId "CUFF.35.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS39"; -chr1 Cufflinks exon 3212718 3212801 . . . transcript_id "TCONS_00000066"; gene_id "XLOC_000036"; exon_number "1"; +chr1 Cufflinks transcript 3212718 3212801 . . . transcript_id "TCONS_00000068"; gene_id "XLOC_000036"; gene_name "Xkr4"; oId "CUFF.35.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS39"; +chr1 Cufflinks exon 3212718 3212801 . . . transcript_id "TCONS_00000068"; gene_id "XLOC_000036"; exon_number "1"; chr1 Cufflinks transcript 3213096 3213192 . . . transcript_id "TCONS_00000026"; gene_id "XLOC_000037"; gene_name "Xkr4"; oId "CUFF.17.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS40"; chr1 Cufflinks exon 3213096 3213192 . . . transcript_id "TCONS_00000026"; gene_id "XLOC_000037"; exon_number "1"; -chr1 Cufflinks transcript 3213119 3213242 . . . transcript_id "TCONS_00000067"; gene_id "XLOC_000037"; gene_name "Xkr4"; oId "CUFF.37.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS40"; -chr1 Cufflinks exon 3213119 3213242 . . . transcript_id "TCONS_00000067"; gene_id "XLOC_000037"; exon_number "1"; -chr1 Cufflinks transcript 3240607 3240633 . . . transcript_id "TCONS_00000068"; gene_id "XLOC_000038"; gene_name "Xkr4"; oId "CUFF.39.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS41"; -chr1 Cufflinks exon 3240607 3240633 . . . transcript_id "TCONS_00000068"; gene_id "XLOC_000038"; exon_number "1"; -chr1 Cufflinks transcript 3242480 3242512 . . . transcript_id "TCONS_00000069"; gene_id "XLOC_000039"; gene_name "Xkr4"; oId "CUFF.41.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS42"; -chr1 Cufflinks exon 3242480 3242512 . . . transcript_id "TCONS_00000069"; gene_id "XLOC_000039"; exon_number "1"; +chr1 Cufflinks transcript 3213119 3213242 . . . transcript_id "TCONS_00000069"; gene_id "XLOC_000037"; gene_name "Xkr4"; oId "CUFF.37.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS40"; +chr1 Cufflinks exon 3213119 3213242 . . . transcript_id "TCONS_00000069"; gene_id "XLOC_000037"; exon_number "1"; +chr1 Cufflinks transcript 3240607 3240633 . . . transcript_id "TCONS_00000070"; gene_id "XLOC_000038"; gene_name "Xkr4"; oId "CUFF.39.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS41"; +chr1 Cufflinks exon 3240607 3240633 . . . transcript_id "TCONS_00000070"; gene_id "XLOC_000038"; exon_number "1"; +chr1 Cufflinks transcript 3242480 3242512 . . . transcript_id "TCONS_00000071"; gene_id "XLOC_000039"; gene_name "Xkr4"; oId "CUFF.41.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS42"; +chr1 Cufflinks exon 3242480 3242512 . . . transcript_id "TCONS_00000071"; gene_id "XLOC_000039"; exon_number "1"; chr1 Cufflinks transcript 3242634 3242923 . . . transcript_id "TCONS_00000027"; gene_id "XLOC_000040"; gene_name "Xkr4"; oId "CUFF.25.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS43"; chr1 Cufflinks exon 3242634 3242923 . . . transcript_id "TCONS_00000027"; gene_id "XLOC_000040"; exon_number "1"; -chr1 Cufflinks transcript 3242925 3243005 . . . transcript_id "TCONS_00000070"; gene_id "XLOC_000041"; gene_name "Xkr4"; oId "CUFF.43.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS44"; -chr1 Cufflinks exon 3242925 3243005 . . . transcript_id "TCONS_00000070"; gene_id "XLOC_000041"; exon_number "1"; +chr1 Cufflinks transcript 3242925 3243005 . . . transcript_id "TCONS_00000072"; gene_id "XLOC_000041"; gene_name "Xkr4"; oId "CUFF.43.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS44"; +chr1 Cufflinks exon 3242925 3243005 . . . transcript_id "TCONS_00000072"; gene_id "XLOC_000041"; exon_number "1"; chr1 Cufflinks transcript 3243019 3243079 . . . transcript_id "TCONS_00000028"; gene_id "XLOC_000042"; gene_name "Xkr4"; oId "CUFF.21.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS45"; chr1 Cufflinks exon 3243019 3243079 . . . transcript_id "TCONS_00000028"; gene_id "XLOC_000042"; exon_number "1"; -chr1 Cufflinks transcript 3243109 3243154 . . . transcript_id "TCONS_00000071"; gene_id "XLOC_000043"; gene_name "Xkr4"; oId "CUFF.45.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS46"; -chr1 Cufflinks exon 3243109 3243154 . . . transcript_id "TCONS_00000071"; gene_id "XLOC_000043"; exon_number "1"; +chr1 Cufflinks transcript 3243109 3243154 . . . transcript_id "TCONS_00000073"; gene_id "XLOC_000043"; gene_name "Xkr4"; oId "CUFF.45.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS46"; +chr1 Cufflinks exon 3243109 3243154 . . . transcript_id "TCONS_00000073"; gene_id "XLOC_000043"; exon_number "1"; chr1 Cufflinks transcript 3243348 3243401 . . . transcript_id "TCONS_00000029"; gene_id "XLOC_000044"; gene_name "Xkr4"; oId "CUFF.23.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS47"; chr1 Cufflinks exon 3243348 3243401 . . . transcript_id "TCONS_00000029"; gene_id "XLOC_000044"; exon_number "1"; -chr1 Cufflinks transcript 3254080 3254106 . . . transcript_id "TCONS_00000072"; gene_id "XLOC_000045"; gene_name "Xkr4"; oId "CUFF.47.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS48"; -chr1 Cufflinks exon 3254080 3254106 . . . transcript_id "TCONS_00000072"; gene_id "XLOC_000045"; exon_number "1"; +chr1 Cufflinks transcript 3254080 3254106 . . . transcript_id "TCONS_00000074"; gene_id "XLOC_000045"; gene_name "Xkr4"; oId "CUFF.47.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS48"; +chr1 Cufflinks exon 3254080 3254106 . . . transcript_id "TCONS_00000074"; gene_id "XLOC_000045"; exon_number "1"; chr1 Cufflinks transcript 3256975 3257011 . . . transcript_id "TCONS_00000030"; gene_id "XLOC_000046"; gene_name "Xkr4"; oId "CUFF.27.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS49"; chr1 Cufflinks exon 3256975 3257011 . . . transcript_id "TCONS_00000030"; gene_id "XLOC_000046"; exon_number "1"; -chr1 Cufflinks transcript 3277156 3277182 . . . transcript_id "TCONS_00000073"; gene_id "XLOC_000047"; gene_name "Xkr4"; oId "CUFF.49.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS50"; -chr1 Cufflinks exon 3277156 3277182 . . . transcript_id "TCONS_00000073"; gene_id "XLOC_000047"; exon_number "1"; +chr1 Cufflinks transcript 3277156 3277182 . . . transcript_id "TCONS_00000075"; gene_id "XLOC_000047"; gene_name "Xkr4"; oId "CUFF.49.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS50"; +chr1 Cufflinks exon 3277156 3277182 . . . transcript_id "TCONS_00000075"; gene_id "XLOC_000047"; exon_number "1"; chr1 Cufflinks transcript 3277191 3277218 . . . transcript_id "TCONS_00000031"; gene_id "XLOC_000048"; gene_name "Xkr4"; oId "CUFF.61.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS51"; chr1 Cufflinks exon 3277191 3277218 . . . transcript_id "TCONS_00000031"; gene_id "XLOC_000048"; exon_number "1"; -chr1 Cufflinks transcript 3277914 3278390 . . . transcript_id "TCONS_00000074"; gene_id "XLOC_000049"; gene_name "Xkr4"; oId "CUFF.51.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS52"; -chr1 Cufflinks exon 3277914 3278390 . . . transcript_id "TCONS_00000074"; gene_id "XLOC_000049"; exon_number "1"; -chr1 Cufflinks transcript 3278237 3278263 . . . transcript_id "TCONS_00000032"; gene_id "XLOC_000049"; gene_name "Xkr4"; oId "CUFF.63.1"; contained_in "TCONS_00000074"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS53"; +chr1 Cufflinks transcript 3277914 3278390 . . . transcript_id "TCONS_00000076"; gene_id "XLOC_000049"; gene_name "Xkr4"; oId "CUFF.51.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS52"; +chr1 Cufflinks exon 3277914 3278390 . . . transcript_id "TCONS_00000076"; gene_id "XLOC_000049"; exon_number "1"; +chr1 Cufflinks transcript 3278237 3278263 . . . transcript_id "TCONS_00000032"; gene_id "XLOC_000049"; gene_name "Xkr4"; oId "CUFF.63.1"; contained_in "TCONS_00000076"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS53"; chr1 Cufflinks exon 3278237 3278263 . . . transcript_id "TCONS_00000032"; gene_id "XLOC_000049"; exon_number "1"; -chr1 Cufflinks transcript 3280118 3280144 . . . transcript_id "TCONS_00000075"; gene_id "XLOC_000050"; gene_name "Xkr4"; oId "CUFF.53.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS54"; -chr1 Cufflinks exon 3280118 3280144 . . . transcript_id "TCONS_00000075"; gene_id "XLOC_000050"; exon_number "1"; -chr1 Cufflinks transcript 3280499 3280525 . . . transcript_id "TCONS_00000076"; gene_id "XLOC_000051"; gene_name "Xkr4"; oId "CUFF.55.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS55"; -chr1 Cufflinks exon 3280499 3280525 . . . transcript_id "TCONS_00000076"; gene_id "XLOC_000051"; exon_number "1"; +chr1 Cufflinks transcript 3280118 3280144 . . . transcript_id "TCONS_00000077"; gene_id "XLOC_000050"; gene_name "Xkr4"; oId "CUFF.53.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS54"; +chr1 Cufflinks exon 3280118 3280144 . . . transcript_id "TCONS_00000077"; gene_id "XLOC_000050"; exon_number "1"; +chr1 Cufflinks transcript 3280499 3280525 . . . transcript_id "TCONS_00000078"; gene_id "XLOC_000051"; gene_name "Xkr4"; oId "CUFF.55.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS55"; +chr1 Cufflinks exon 3280499 3280525 . . . transcript_id "TCONS_00000078"; gene_id "XLOC_000051"; exon_number "1"; chr1 Cufflinks transcript 3280687 3280741 . . . transcript_id "TCONS_00000033"; gene_id "XLOC_000052"; gene_name "Xkr4"; oId "CUFF.65.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS56"; chr1 Cufflinks exon 3280687 3280741 . . . transcript_id "TCONS_00000033"; gene_id "XLOC_000052"; exon_number "1"; -chr1 Cufflinks transcript 3282505 3282531 . . . transcript_id "TCONS_00000077"; gene_id "XLOC_000053"; gene_name "Xkr4"; oId "CUFF.57.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS57"; -chr1 Cufflinks exon 3282505 3282531 . . . transcript_id "TCONS_00000077"; gene_id "XLOC_000053"; exon_number "1"; -chr1 Cufflinks transcript 3282651 3282677 . . . transcript_id "TCONS_00000078"; gene_id "XLOC_000054"; gene_name "Xkr4"; oId "CUFF.59.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS58"; -chr1 Cufflinks exon 3282651 3282677 . . . transcript_id "TCONS_00000078"; gene_id "XLOC_000054"; exon_number "1"; -chr1 Cufflinks transcript 3282761 3282832 . . . transcript_id "TCONS_00000079"; gene_id "XLOC_000055"; gene_name "Xkr4"; oId "CUFF.61.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS59"; -chr1 Cufflinks exon 3282761 3282832 . . . transcript_id "TCONS_00000079"; gene_id "XLOC_000055"; exon_number "1"; -chr1 Cufflinks transcript 3284967 3284993 . . . transcript_id "TCONS_00000080"; gene_id "XLOC_000056"; gene_name "Xkr4"; oId "CUFF.63.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS60"; -chr1 Cufflinks exon 3284967 3284993 . . . transcript_id "TCONS_00000080"; gene_id "XLOC_000056"; exon_number "1"; +chr1 Cufflinks transcript 3282505 3282531 . . . transcript_id "TCONS_00000079"; gene_id "XLOC_000053"; gene_name "Xkr4"; oId "CUFF.57.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS57"; +chr1 Cufflinks exon 3282505 3282531 . . . transcript_id "TCONS_00000079"; gene_id "XLOC_000053"; exon_number "1"; +chr1 Cufflinks transcript 3282651 3282677 . . . transcript_id "TCONS_00000080"; gene_id "XLOC_000054"; gene_name "Xkr4"; oId "CUFF.59.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS58"; +chr1 Cufflinks exon 3282651 3282677 . . . transcript_id "TCONS_00000080"; gene_id "XLOC_000054"; exon_number "1"; +chr1 Cufflinks transcript 3282761 3282832 . . . transcript_id "TCONS_00000081"; gene_id "XLOC_000055"; gene_name "Xkr4"; oId "CUFF.61.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS59"; +chr1 Cufflinks exon 3282761 3282832 . . . transcript_id "TCONS_00000081"; gene_id "XLOC_000055"; exon_number "1"; +chr1 Cufflinks transcript 3284967 3284993 . . . transcript_id "TCONS_00000082"; gene_id "XLOC_000056"; gene_name "Xkr4"; oId "CUFF.63.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS60"; +chr1 Cufflinks exon 3284967 3284993 . . . transcript_id "TCONS_00000082"; gene_id "XLOC_000056"; exon_number "1"; chr1 Cufflinks transcript 3290489 3290553 . . . transcript_id "TCONS_00000034"; gene_id "XLOC_000057"; gene_name "Xkr4"; oId "CUFF.67.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS61"; chr1 Cufflinks exon 3290489 3290553 . . . transcript_id "TCONS_00000034"; gene_id "XLOC_000057"; exon_number "1"; -chr1 Cufflinks transcript 3290799 3290859 . . . transcript_id "TCONS_00000081"; gene_id "XLOC_000058"; gene_name "Xkr4"; oId "CUFF.65.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS62"; -chr1 Cufflinks exon 3290799 3290859 . . . transcript_id "TCONS_00000081"; gene_id "XLOC_000058"; exon_number "1"; -chr1 Cufflinks transcript 3290920 3291273 . . . transcript_id "TCONS_00000082"; gene_id "XLOC_000059"; gene_name "Xkr4"; oId "CUFF.69.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS63"; -chr1 Cufflinks exon 3290920 3291273 . . . transcript_id "TCONS_00000082"; gene_id "XLOC_000059"; exon_number "1"; -chr1 Cufflinks transcript 3290940 3291023 . . . transcript_id "TCONS_00000035"; gene_id "XLOC_000059"; gene_name "Xkr4"; oId "CUFF.69.1"; contained_in "TCONS_00000082"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS63"; +chr1 Cufflinks transcript 3290799 3290859 . . . transcript_id "TCONS_00000083"; gene_id "XLOC_000058"; gene_name "Xkr4"; oId "CUFF.65.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS62"; +chr1 Cufflinks exon 3290799 3290859 . . . transcript_id "TCONS_00000083"; gene_id "XLOC_000058"; exon_number "1"; +chr1 Cufflinks transcript 3290920 3291273 . . . transcript_id "TCONS_00000084"; gene_id "XLOC_000059"; gene_name "Xkr4"; oId "CUFF.69.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS63"; +chr1 Cufflinks exon 3290920 3291273 . . . transcript_id "TCONS_00000084"; gene_id "XLOC_000059"; exon_number "1"; +chr1 Cufflinks transcript 3290940 3291023 . . . transcript_id "TCONS_00000035"; gene_id "XLOC_000059"; gene_name "Xkr4"; oId "CUFF.69.1"; contained_in "TCONS_00000084"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS63"; chr1 Cufflinks exon 3290940 3291023 . . . transcript_id "TCONS_00000035"; gene_id "XLOC_000059"; exon_number "1"; -chr1 Cufflinks transcript 3291089 3291186 . . . transcript_id "TCONS_00000036"; gene_id "XLOC_000059"; gene_name "Xkr4"; oId "CUFF.71.1"; contained_in "TCONS_00000082"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS64"; +chr1 Cufflinks transcript 3291089 3291186 . . . transcript_id "TCONS_00000036"; gene_id "XLOC_000059"; gene_name "Xkr4"; oId "CUFF.71.1"; contained_in "TCONS_00000084"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS64"; chr1 Cufflinks exon 3291089 3291186 . . . transcript_id "TCONS_00000036"; gene_id "XLOC_000059"; exon_number "1"; -chr1 Cufflinks transcript 3299444 3299640 . . . transcript_id "TCONS_00000083"; gene_id "XLOC_000060"; gene_name "Xkr4"; oId "CUFF.67.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS65"; -chr1 Cufflinks exon 3299444 3299640 . . . transcript_id "TCONS_00000083"; gene_id "XLOC_000060"; exon_number "1"; +chr1 Cufflinks transcript 3299444 3299640 . . . transcript_id "TCONS_00000085"; gene_id "XLOC_000060"; gene_name "Xkr4"; oId "CUFF.67.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS65"; +chr1 Cufflinks exon 3299444 3299640 . . . transcript_id "TCONS_00000085"; gene_id "XLOC_000060"; exon_number "1"; chr1 Cufflinks transcript 3299610 3299664 . . . transcript_id "TCONS_00000037"; gene_id "XLOC_000060"; gene_name "Xkr4"; oId "CUFF.73.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS66"; chr1 Cufflinks exon 3299610 3299664 . . . transcript_id "TCONS_00000037"; gene_id "XLOC_000060"; exon_number "1"; -chr1 Cufflinks transcript 3299692 3299733 . . . transcript_id "TCONS_00000084"; gene_id "XLOC_000061"; gene_name "Xkr4"; oId "CUFF.71.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS67"; -chr1 Cufflinks exon 3299692 3299733 . . . transcript_id "TCONS_00000084"; gene_id "XLOC_000061"; exon_number "1"; +chr1 Cufflinks transcript 3299692 3299733 . . . transcript_id "TCONS_00000086"; gene_id "XLOC_000061"; gene_name "Xkr4"; oId "CUFF.71.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS67"; +chr1 Cufflinks exon 3299692 3299733 . . . transcript_id "TCONS_00000086"; gene_id "XLOC_000061"; exon_number "1"; chr1 Cufflinks transcript 3300052 3300078 . . . transcript_id "TCONS_00000038"; gene_id "XLOC_000062"; gene_name "Xkr4"; oId "CUFF.75.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS68"; chr1 Cufflinks exon 3300052 3300078 . . . transcript_id "TCONS_00000038"; gene_id "XLOC_000062"; exon_number "1"; -chr1 Cufflinks transcript 3307749 3307775 . . . transcript_id "TCONS_00000085"; gene_id "XLOC_000063"; gene_name "Xkr4"; oId "CUFF.73.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS69"; -chr1 Cufflinks exon 3307749 3307775 . . . transcript_id "TCONS_00000085"; gene_id "XLOC_000063"; exon_number "1"; -chr1 Cufflinks transcript 3318621 3318647 . . . transcript_id "TCONS_00000086"; gene_id "XLOC_000064"; gene_name "Xkr4"; oId "CUFF.75.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS70"; -chr1 Cufflinks exon 3318621 3318647 . . . transcript_id "TCONS_00000086"; gene_id "XLOC_000064"; exon_number "1"; +chr1 Cufflinks transcript 3307749 3307775 . . . transcript_id "TCONS_00000087"; gene_id "XLOC_000063"; gene_name "Xkr4"; oId "CUFF.73.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS69"; +chr1 Cufflinks exon 3307749 3307775 . . . transcript_id "TCONS_00000087"; gene_id "XLOC_000063"; exon_number "1"; +chr1 Cufflinks transcript 3318621 3318647 . . . transcript_id "TCONS_00000088"; gene_id "XLOC_000064"; gene_name "Xkr4"; oId "CUFF.75.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS70"; +chr1 Cufflinks exon 3318621 3318647 . . . transcript_id "TCONS_00000088"; gene_id "XLOC_000064"; exon_number "1"; chr1 Cufflinks transcript 3319000 3319051 . . . transcript_id "TCONS_00000039"; gene_id "XLOC_000065"; gene_name "Xkr4"; oId "CUFF.77.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS71"; chr1 Cufflinks exon 3319000 3319051 . . . transcript_id "TCONS_00000039"; gene_id "XLOC_000065"; exon_number "1"; -chr1 Cufflinks transcript 3330528 3330554 . . . transcript_id "TCONS_00000087"; gene_id "XLOC_000066"; gene_name "Xkr4"; oId "CUFF.77.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS72"; -chr1 Cufflinks exon 3330528 3330554 . . . transcript_id "TCONS_00000087"; gene_id "XLOC_000066"; exon_number "1"; -chr1 Cufflinks transcript 3351241 3351311 . . . transcript_id "TCONS_00000088"; gene_id "XLOC_000067"; gene_name "Xkr4"; oId "CUFF.79.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS73"; -chr1 Cufflinks exon 3351241 3351311 . . . transcript_id "TCONS_00000088"; gene_id "XLOC_000067"; exon_number "1"; +chr1 Cufflinks transcript 3330528 3330554 . . . transcript_id "TCONS_00000089"; gene_id "XLOC_000066"; gene_name "Xkr4"; oId "CUFF.77.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS72"; +chr1 Cufflinks exon 3330528 3330554 . . . transcript_id "TCONS_00000089"; gene_id "XLOC_000066"; exon_number "1"; +chr1 Cufflinks transcript 3351241 3351311 . . . transcript_id "TCONS_00000090"; gene_id "XLOC_000067"; gene_name "Xkr4"; oId "CUFF.79.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS73"; +chr1 Cufflinks exon 3351241 3351311 . . . transcript_id "TCONS_00000090"; gene_id "XLOC_000067"; exon_number "1"; chr1 Cufflinks transcript 3355888 3355914 . . . transcript_id "TCONS_00000040"; gene_id "XLOC_000068"; gene_name "Xkr4"; oId "CUFF.79.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS74"; chr1 Cufflinks exon 3355888 3355914 . . . transcript_id "TCONS_00000040"; gene_id "XLOC_000068"; exon_number "1"; -chr1 Cufflinks transcript 3355908 3356119 . . . transcript_id "TCONS_00000089"; gene_id "XLOC_000068"; gene_name "Xkr4"; oId "CUFF.81.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS74"; -chr1 Cufflinks exon 3355908 3356119 . . . transcript_id "TCONS_00000089"; gene_id "XLOC_000068"; exon_number "1"; -chr1 Cufflinks transcript 3356181 3356225 . . . transcript_id "TCONS_00000090"; gene_id "XLOC_000069"; gene_name "Xkr4"; oId "CUFF.83.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS75"; -chr1 Cufflinks exon 3356181 3356225 . . . transcript_id "TCONS_00000090"; gene_id "XLOC_000069"; exon_number "1"; -chr1 Cufflinks transcript 3363077 3363176 . . . transcript_id "TCONS_00000091"; gene_id "XLOC_000070"; gene_name "Xkr4"; oId "CUFF.85.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS76"; -chr1 Cufflinks exon 3363077 3363176 . . . transcript_id "TCONS_00000091"; gene_id "XLOC_000070"; exon_number "1"; +chr1 Cufflinks transcript 3355908 3356119 . . . transcript_id "TCONS_00000091"; gene_id "XLOC_000068"; gene_name "Xkr4"; oId "CUFF.81.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS74"; +chr1 Cufflinks exon 3355908 3356119 . . . transcript_id "TCONS_00000091"; gene_id "XLOC_000068"; exon_number "1"; +chr1 Cufflinks transcript 3356181 3356225 . . . transcript_id "TCONS_00000092"; gene_id "XLOC_000069"; gene_name "Xkr4"; oId "CUFF.83.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS75"; +chr1 Cufflinks exon 3356181 3356225 . . . transcript_id "TCONS_00000092"; gene_id "XLOC_000069"; exon_number "1"; +chr1 Cufflinks transcript 3363077 3363176 . . . transcript_id "TCONS_00000093"; gene_id "XLOC_000070"; gene_name "Xkr4"; oId "CUFF.85.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS76"; +chr1 Cufflinks exon 3363077 3363176 . . . transcript_id "TCONS_00000093"; gene_id "XLOC_000070"; exon_number "1"; chr1 Cufflinks transcript 3363215 3363278 . . . transcript_id "TCONS_00000041"; gene_id "XLOC_000071"; gene_name "Xkr4"; oId "CUFF.81.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS77"; chr1 Cufflinks exon 3363215 3363278 . . . transcript_id "TCONS_00000041"; gene_id "XLOC_000071"; exon_number "1"; -chr1 Cufflinks transcript 3363388 3363446 . . . transcript_id "TCONS_00000092"; gene_id "XLOC_000072"; gene_name "Xkr4"; oId "CUFF.87.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS78"; -chr1 Cufflinks exon 3363388 3363446 . . . transcript_id "TCONS_00000092"; gene_id "XLOC_000072"; exon_number "1"; +chr1 Cufflinks transcript 3363388 3363446 . . . transcript_id "TCONS_00000094"; gene_id "XLOC_000072"; gene_name "Xkr4"; oId "CUFF.87.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS78"; +chr1 Cufflinks exon 3363388 3363446 . . . transcript_id "TCONS_00000094"; gene_id "XLOC_000072"; exon_number "1"; chr1 Cufflinks transcript 3363754 3363849 . . . transcript_id "TCONS_00000042"; gene_id "XLOC_000073"; gene_name "Xkr4"; oId "CUFF.83.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS79"; chr1 Cufflinks exon 3363754 3363849 . . . transcript_id "TCONS_00000042"; gene_id "XLOC_000073"; exon_number "1"; -chr1 Cufflinks transcript 3364872 3364919 . . . transcript_id "TCONS_00000093"; gene_id "XLOC_000074"; gene_name "Xkr4"; oId "CUFF.89.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS80"; -chr1 Cufflinks exon 3364872 3364919 . . . transcript_id "TCONS_00000093"; gene_id "XLOC_000074"; exon_number "1"; +chr1 Cufflinks transcript 3364872 3364919 . . . transcript_id "TCONS_00000095"; gene_id "XLOC_000074"; gene_name "Xkr4"; oId "CUFF.89.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS80"; +chr1 Cufflinks exon 3364872 3364919 . . . transcript_id "TCONS_00000095"; gene_id "XLOC_000074"; exon_number "1"; chr1 Cufflinks transcript 3367136 3367162 . . . transcript_id "TCONS_00000043"; gene_id "XLOC_000075"; gene_name "Xkr4"; oId "CUFF.85.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS81"; chr1 Cufflinks exon 3367136 3367162 . . . transcript_id "TCONS_00000043"; gene_id "XLOC_000075"; exon_number "1"; -chr1 Cufflinks transcript 3367211 3367237 . . . transcript_id "TCONS_00000094"; gene_id "XLOC_000076"; gene_name "Xkr4"; oId "CUFF.91.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS82"; -chr1 Cufflinks exon 3367211 3367237 . . . transcript_id "TCONS_00000094"; gene_id "XLOC_000076"; exon_number "1"; +chr1 Cufflinks transcript 3367211 3367237 . . . transcript_id "TCONS_00000096"; gene_id "XLOC_000076"; gene_name "Xkr4"; oId "CUFF.91.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS82"; +chr1 Cufflinks exon 3367211 3367237 . . . transcript_id "TCONS_00000096"; gene_id "XLOC_000076"; exon_number "1"; chr1 Cufflinks transcript 3367334 3367382 . . . transcript_id "TCONS_00000044"; gene_id "XLOC_000077"; gene_name "Xkr4"; oId "CUFF.87.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS83"; chr1 Cufflinks exon 3367334 3367382 . . . transcript_id "TCONS_00000044"; gene_id "XLOC_000077"; exon_number "1"; -chr1 Cufflinks transcript 3369581 3369607 . . . transcript_id "TCONS_00000095"; gene_id "XLOC_000078"; gene_name "Xkr4"; oId "CUFF.93.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS84"; -chr1 Cufflinks exon 3369581 3369607 . . . transcript_id "TCONS_00000095"; gene_id "XLOC_000078"; exon_number "1"; -chr1 Cufflinks transcript 3375002 3375028 . . . transcript_id "TCONS_00000096"; gene_id "XLOC_000079"; gene_name "Xkr4"; oId "CUFF.95.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS85"; -chr1 Cufflinks exon 3375002 3375028 . . . transcript_id "TCONS_00000096"; gene_id "XLOC_000079"; exon_number "1"; +chr1 Cufflinks transcript 3369581 3369607 . . . transcript_id "TCONS_00000097"; gene_id "XLOC_000078"; gene_name "Xkr4"; oId "CUFF.93.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS84"; +chr1 Cufflinks exon 3369581 3369607 . . . transcript_id "TCONS_00000097"; gene_id "XLOC_000078"; exon_number "1"; +chr1 Cufflinks transcript 3375002 3375028 . . . transcript_id "TCONS_00000098"; gene_id "XLOC_000079"; gene_name "Xkr4"; oId "CUFF.95.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS85"; +chr1 Cufflinks exon 3375002 3375028 . . . transcript_id "TCONS_00000098"; gene_id "XLOC_000079"; exon_number "1"; chr1 Cufflinks transcript 3377212 3377262 . . . transcript_id "TCONS_00000045"; gene_id "XLOC_000080"; gene_name "Xkr4"; oId "CUFF.89.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS86"; chr1 Cufflinks exon 3377212 3377262 . . . transcript_id "TCONS_00000045"; gene_id "XLOC_000080"; exon_number "1"; -chr1 Cufflinks transcript 3379889 3379915 . . . transcript_id "TCONS_00000097"; gene_id "XLOC_000081"; gene_name "Xkr4"; oId "CUFF.97.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS87"; -chr1 Cufflinks exon 3379889 3379915 . . . transcript_id "TCONS_00000097"; gene_id "XLOC_000081"; exon_number "1"; -chr1 Cufflinks transcript 3386740 3386836 . . . transcript_id "TCONS_00000098"; gene_id "XLOC_000082"; gene_name "Xkr4"; oId "CUFF.99.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS88"; -chr1 Cufflinks exon 3386740 3386836 . . . transcript_id "TCONS_00000098"; gene_id "XLOC_000082"; exon_number "1"; +chr1 Cufflinks transcript 3379889 3379915 . . . transcript_id "TCONS_00000099"; gene_id "XLOC_000081"; gene_name "Xkr4"; oId "CUFF.97.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS87"; +chr1 Cufflinks exon 3379889 3379915 . . . transcript_id "TCONS_00000099"; gene_id "XLOC_000081"; exon_number "1"; +chr1 Cufflinks transcript 3386740 3386836 . . . transcript_id "TCONS_00000100"; gene_id "XLOC_000082"; gene_name "Xkr4"; oId "CUFF.99.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS88"; +chr1 Cufflinks exon 3386740 3386836 . . . transcript_id "TCONS_00000100"; gene_id "XLOC_000082"; exon_number "1"; chr1 Cufflinks transcript 3391326 3391352 . . . transcript_id "TCONS_00000046"; gene_id "XLOC_000083"; gene_name "Xkr4"; oId "CUFF.91.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS89"; chr1 Cufflinks exon 3391326 3391352 . . . transcript_id "TCONS_00000046"; gene_id "XLOC_000083"; exon_number "1"; chr1 Cufflinks transcript 3435842 3435880 . . . transcript_id "TCONS_00000047"; gene_id "XLOC_000084"; gene_name "Xkr4"; oId "CUFF.93.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS90";
--- 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 @@ -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)
--- 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 @@ -1,98 +1,100 @@ -TCONS_00000001 XLOC_000001 Xkr4|Xkr4 c q1:CUFF.13|CUFF.13.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000002 XLOC_000002 - u q1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000003 XLOC_000003 - u q1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|- - -TCONS_00000004 XLOC_000007 - u q1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|- - -TCONS_00000005 XLOC_000007 - u q1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|- - -TCONS_00000006 XLOC_000007 - u q1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|- - -TCONS_00000007 XLOC_000009 - u q1:CUFF.35|CUFF.35.1|100|96.747183|61.420107|132.074259|6.183206|- - -TCONS_00000008 XLOC_000009 - u q1:CUFF.37|CUFF.37.1|100|104.085013|53.596365|154.573660|6.652174|- - -TCONS_00000009 XLOC_000011 - u q1:CUFF.39|CUFF.39.1|100|23.912983|0.000000|51.525317|1.528302|- - -TCONS_00000010 XLOC_000012 - u q1:CUFF.41|CUFF.41.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000011 XLOC_000014 - u q1:CUFF.43|CUFF.43.1|100|10.561567|0.000000|25.497879|0.675000|- - -TCONS_00000012 XLOC_000015 - u q1:CUFF.45|CUFF.45.1|100|20.708956|2.186303|39.231609|1.323529|- - -TCONS_00000013 XLOC_000016 - u q1:CUFF.47|CUFF.47.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000014 XLOC_000017 - u q1:CUFF.49|CUFF.49.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000015 XLOC_000019 - u q1:CUFF.51|CUFF.51.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000016 XLOC_000020 - u q1:CUFF.53|CUFF.53.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000017 XLOC_000021 - u q1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000018 XLOC_000022 - u q1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000019 XLOC_000023 - u q1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000020 XLOC_000025 - u q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|169 q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|88 -TCONS_00000021 XLOC_000026 - u q1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000022 XLOC_000029 - u q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|404 q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|27 -TCONS_00000023 XLOC_000031 - u q1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000024 XLOC_000034 Xkr4|Xkr4 i q1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000025 XLOC_000035 Xkr4|Xkr4 i q1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|- - -TCONS_00000026 XLOC_000037 Xkr4|Xkr4 i q1:CUFF.17|CUFF.17.1|100|8.710571|0.000000|21.029179|0.556701|- - -TCONS_00000027 XLOC_000040 Xkr4|Xkr4 i q1:CUFF.25|CUFF.25.1|100|14.567679|5.354270|23.781089|0.931034|- - -TCONS_00000028 XLOC_000042 Xkr4|Xkr4 i q1:CUFF.21|CUFF.21.1|100|13.851236|0.000000|33.439842|0.885246|- - -TCONS_00000029 XLOC_000044 Xkr4|Xkr4 i q1:CUFF.23|CUFF.23.1|100|23.470150|0.000000|50.571145|1.500000|- - -TCONS_00000030 XLOC_000046 Xkr4|Xkr4 i q1:CUFF.27|CUFF.27.1|100|34.253732|0.000000|73.806535|2.189189|- - -TCONS_00000031 XLOC_000048 Xkr4|Xkr4 i q1:CUFF.61|CUFF.61.1|100|45.263860|0.000000|97.530065|2.892857|- - -TCONS_00000032 XLOC_000049 Xkr4|Xkr4 i q1:CUFF.63|CUFF.63.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000033 XLOC_000052 Xkr4|Xkr4 i q1:CUFF.65|CUFF.65.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000034 XLOC_000057 Xkr4|Xkr4 i q1:CUFF.67|CUFF.67.1|100|12.998852|0.000000|31.382005|0.830769|- - -TCONS_00000035 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.69|CUFF.69.1|100|10.058636|0.000000|24.283695|0.642857|- - -TCONS_00000036 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.71|CUFF.71.1|100|8.621688|0.000000|20.814595|0.551020|- - -TCONS_00000037 XLOC_000060 Xkr4|Xkr4 i q1:CUFF.73|CUFF.73.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000038 XLOC_000062 Xkr4|Xkr4 i q1:CUFF.75|CUFF.75.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000039 XLOC_000065 Xkr4|Xkr4 i q1:CUFF.77|CUFF.77.1|100|16.248565|0.000000|39.227507|1.038462|- - -TCONS_00000040 XLOC_000068 Xkr4|Xkr4 i q1:CUFF.79|CUFF.79.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000041 XLOC_000071 Xkr4|Xkr4 i q1:CUFF.81|CUFF.81.1|100|13.201959|0.000000|31.872349|0.843750|- - -TCONS_00000042 XLOC_000073 Xkr4|Xkr4 i q1:CUFF.83|CUFF.83.1|100|13.201959|0.000000|28.446269|0.843750|- - -TCONS_00000043 XLOC_000075 Xkr4|Xkr4 i q1:CUFF.85|CUFF.85.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000044 XLOC_000077 Xkr4|Xkr4 i q1:CUFF.87|CUFF.87.1|100|17.243375|0.000000|41.629191|1.102041|- - -TCONS_00000045 XLOC_000080 Xkr4|Xkr4 i q1:CUFF.89|CUFF.89.1|100|16.567165|0.000000|39.996674|1.058824|- - -TCONS_00000046 XLOC_000083 Xkr4|Xkr4 i q1:CUFF.91|CUFF.91.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000047 XLOC_000084 Xkr4|Xkr4 i q1:CUFF.93|CUFF.93.1|100|21.664754|0.000000|52.303342|1.384615|- - -TCONS_00000048 XLOC_000085 Xkr4|Xkr4 i q1:CUFF.95|CUFF.95.1|100|46.940300|0.000000|101.142289|3.000000|- - -TCONS_00000049 XLOC_000086 Xkr4|Xkr4 i q1:CUFF.97|CUFF.97.1|100|21.481154|0.000000|46.285454|1.372881|- - -TCONS_00000050 XLOC_000087 Xkr4|Xkr4 i q1:CUFF.99|CUFF.99.1|100|14.567679|0.000000|35.169489|0.931034|- - -TCONS_00000051 XLOC_000004 - u - q2:CUFF.1|CUFF.1.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000052 XLOC_000005 - u - q2:CUFF.3|CUFF.3.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000053 XLOC_000006 - u - q2:CUFF.5|CUFF.5.1|100|21.226627|0.000000|59.889707|1.205672|- -TCONS_00000054 XLOC_000007 - u - q2:CUFF.11|CUFF.11.1|100|32.531777|24.582998|40.480555|1.847804|- -TCONS_00000055 XLOC_000008 - u - q2:CUFF.7|CUFF.7.1|100|29.709524|19.806349|39.612698|1.687500|- -TCONS_00000056 XLOC_000009 - u - q2:CUFF.9|CUFF.9.1|100|34.072933|23.364686|44.781179|1.935341|- -TCONS_00000057 XLOC_000010 - u - q2:CUFF.13|CUFF.13.1|100|16.582060|0.000000|35.729373|0.941860|- -TCONS_00000058 XLOC_000013 - u - q2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000059 XLOC_000018 - u - q2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000060 XLOC_000024 - u - q2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000061 XLOC_000027 - u - q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000062 XLOC_000028 - u - q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|- -TCONS_00000063 XLOC_000030 - u - q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|- -TCONS_00000064 XLOC_000032 - u - q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|- -TCONS_00000065 XLOC_000033 Xkr4|Xkr4 i - q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|- -TCONS_00000066 XLOC_000036 Xkr4|Xkr4 i - q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|- -TCONS_00000067 XLOC_000037 Xkr4|Xkr4 i - q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|- -TCONS_00000068 XLOC_000038 Xkr4|Xkr4 i - q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000069 XLOC_000039 Xkr4|Xkr4 i - 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q2:CUFF.61|CUFF.61.1|1|13.204233|0.000000|0.750000|72 +TCONS_00000082 XLOC_000056 Xkr4|Xkr4 i - q2:CUFF.63|CUFF.63.1|1|35.211287|0.000000|2.000000|27 +TCONS_00000083 XLOC_000058 Xkr4|Xkr4 i - q2:CUFF.65|CUFF.65.1|1|31.170648|0.000000|1.770492|61 +TCONS_00000084 XLOC_000059 Xkr4|Xkr4 i - q2:CUFF.69|CUFF.69.1|1|18.799247|0.000000|1.067797|354 +TCONS_00000085 XLOC_000060 Xkr4|Xkr4 i - q2:CUFF.67|CUFF.67.1|1|15.681351|0.000000|0.890700|197 +TCONS_00000086 XLOC_000061 Xkr4|Xkr4 i - q2:CUFF.71|CUFF.71.1|1|22.635827|0.000000|1.285714|42 +TCONS_00000087 XLOC_000063 Xkr4|Xkr4 i - q2:CUFF.73|CUFF.73.1|1|35.211287|0.000000|2.000000|27 +TCONS_00000088 XLOC_000064 Xkr4|Xkr4 i - q2:CUFF.75|CUFF.75.1|1|52.816931|0.000000|3.000000|27 +TCONS_00000089 XLOC_000066 Xkr4|Xkr4 i - q2:CUFF.77|CUFF.77.1|1|17.605644|0.000000|1.000000|27 +TCONS_00000090 XLOC_000067 Xkr4|Xkr4 i - q2:CUFF.79|CUFF.79.1|1|13.390208|0.000000|0.760563|71 +TCONS_00000091 XLOC_000068 Xkr4|Xkr4 i - q2:CUFF.81|CUFF.81.1|1|11.211141|0.000000|0.636792|212 +TCONS_00000092 XLOC_000069 Xkr4|Xkr4 i - q2:CUFF.83|CUFF.83.1|1|21.126772|0.000000|1.200000|45 +TCONS_00000093 XLOC_000070 Xkr4|Xkr4 i - q2:CUFF.85|CUFF.85.1|1|19.014095|0.000000|1.080000|100 +TCONS_00000094 XLOC_000072 Xkr4|Xkr4 i - q2:CUFF.87|CUFF.87.1|1|24.170460|0.000000|1.372881|59 +TCONS_00000095 XLOC_000074 Xkr4|Xkr4 i - q2:CUFF.89|CUFF.89.1|1|29.709524|0.000000|1.687500|48 +TCONS_00000096 XLOC_000076 Xkr4|Xkr4 i - q2:CUFF.91|CUFF.91.1|1|35.211287|0.000000|2.000000|27 +TCONS_00000097 XLOC_000078 Xkr4|Xkr4 i - q2:CUFF.93|CUFF.93.1|1|35.211287|0.000000|2.000000|27 +TCONS_00000098 XLOC_000079 Xkr4|Xkr4 i - q2:CUFF.95|CUFF.95.1|1|35.211287|0.000000|2.000000|27 +TCONS_00000099 XLOC_000081 Xkr4|Xkr4 i - q2:CUFF.97|CUFF.97.1|1|35.211287|0.000000|2.000000|27 +TCONS_00000100 XLOC_000082 Xkr4|Xkr4 i - q2:CUFF.99|CUFF.99.1|1|19.602160|0.000000|1.113402|97
--- 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 @@ -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";
--- 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 @@ -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)
--- 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 @@ -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