| Next changeset 1:c80cdc2eac6d (2018-12-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/gffcompare commit 33ef7ef2f829bf46a6fde7637715d974c17f898a |
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added:
gffcompare.xml test-data/gffcompare_in1.gtf test-data/gffcompare_in2.gtf test-data/gffcompare_in3.gtf test-data/gffcompare_in4.gtf test-data/gffcompare_in5.gtf test-data/gffcompare_out1.gtf test-data/gffcompare_out1.loci test-data/gffcompare_out1.stats test-data/gffcompare_out1.tracking test-data/gffcompare_out2.gtf test-data/gffcompare_out2.loci test-data/gffcompare_out2.stats test-data/gffcompare_out2.tracking tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 3c97c841a443 gffcompare.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gffcompare.xml Fri Apr 07 16:02:07 2017 -0400 |
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| b'@@ -0,0 +1,164 @@\n+<tool id="gffcompare" name="GffCompare" version="0.9.8">\n+ <description>compare assembled transcripts to a reference annotation</description>\n+ <requirements>\n+ <requirement type="package" version="0.9.8">gffcompare</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ <regex match="Error" />\n+ <regex match="Exception" />\n+ </stdio>\n+ <version_command>gffcompare -v | awk \'{print $2}\'</version_command>\n+ <command>\n+ <![CDATA[\n+ #set $input_gtf = "\' \'".join(str($inputs).split(\',\'))\n+ #if $seq_data.use_seq_data == "Yes":\n+ #if $seq_data.seq_source.index_source == "history":\n+ ln -s \'$seq_data.seq_source.ref_file\' ref_seq.fa &&\n+ #else:\n+ ln -s \'${seq_data.seq_source.index.fields.path}\' ref_seq.fa &&\n+ #end if\n+ #end if\n+ gffcompare\n+ ## Use annotation reference?\n+ #if $annotation.use_ref_annotation == "Yes":\n+ -r \'$annotation.reference_annotation\' $annotation.ignore_nonoverlapping_reference $annotation.ignore_nonoverlapping_transfrags\n+ #end if\n+\n+ ## Use sequence data?\n+\n+ #if $seq_data.use_seq_data == "Yes":\n+ -s ref_seq.fa\n+ #end if\n+\n+ $discard_single_exon -e $max_dist_exon -d $max_dist_group $discard_intron_redundant_transfrags\n+\n+ \'$input_gtf\'\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param format="gtf" name="inputs" type="data" label="GTF inputs for comparison" help="" multiple="true" />\n+ <conditional name="annotation">\n+ <param label="Use Reference Annotation" name="use_ref_annotation" type="select">\n+ <option value="No">No</option>\n+ <option value="Yes">Yes</option>\n+ </param>\n+ <when value="Yes">\n+ <param argument="-r" format="gff3,gtf" help="Requires an annotation file in GFF3 or GTF format." label="Reference Annotation" name="reference_annotation" type="data" />\n+ <param argument="-R" falsevalue="" help="consider only the reference transcripts that overlap any of the input transfrags (Sn correction)" label="Ignore reference transcripts that are not overlapped by any input transfrags" name="ignore_nonoverlapping_reference" truevalue="-R" type="boolean" />\n+ <param argument="-Q" falsevalue="" help="consider only the input transcripts that overlap any of the reference transcripts (Sp correction). Warning: this will discard all \'novel\' loci!" label="Ignore input transcripts that are not overlapped by any reference transcripts" name="ignore_nonoverlapping_transfrags" truevalue="-Q" type="boolean" />\n+ </when>\n+ <when value="No">\n+ </when>\n+ </conditional>\n+ <conditional name="seq_data">\n+ <param help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff." label="Use Sequence Data" name="use_seq_data" type="select">\n+ <option value="Yes">Yes</option>\n+ <option value="No">No</option>\n+ </param>\n+ <when value="No" />\n+ <when value="Yes">\n+ <conditional name="seq_source">\n+ <param label="Choose the source for the reference list" name="index_source" type="select">\n+ <option value="cached">Locally cached</option>\n+ <option value="history">History</option>\n+ </param>\n+ <when value="cached">\n+ <param argument="-s" label="Using reference genome" name="index" type="select">\n+ <options from_data_table="fasta_indexes">\n+ <filter column="1" key="dbkey" ref="'..b'>\n+ <param name="use_ref_annotation" value="Yes" />\n+ <param ftype="gtf" name="reference_annotation" value="gffcompare_in3.gtf" />\n+ <param name="ignore_nonoverlapping_reference" value="Yes" />\n+ <param name="ignore_nonoverlapping_transfrags" value="No" />\n+ <param name="use_seq_data" value="No" />\n+ <param name="discard_single_exon" value="" />\n+ <param name="max_dist_exon" value="100" />\n+ <param name="max_dist_group" value="100" />\n+ <param name="discard_intron_redundant_transfrags" value="No" />\n+ <output file="gffcompare_out1.stats" name="transcripts_stats" lines_diff="6" />\n+ <output file="gffcompare_out1.loci" name="transcripts_loci" />\n+ <output file="gffcompare_out1.tracking" name="transcripts_tracking" />\n+ <output file="gffcompare_out1.gtf" name="transcripts_combined" />\n+ </test>\n+ <test>\n+ <param ftype="gtf" name="inputs" value="gffcompare_in4.gtf" />\n+ <param name="use_ref_annotation" value="Yes" />\n+ <param ftype="gtf" name="reference_annotation" value="gffcompare_in5.gtf" />\n+ <param name="ignore_nonoverlapping_reference" value="Yes" />\n+ <param name="ignore_nonoverlapping_transfrags" value="No" />\n+ <param name="use_seq_data" value="No" />\n+ <param name="discard_single_exon" value="" />\n+ <param name="max_dist_exon" value="100" />\n+ <param name="max_dist_group" value="100" />\n+ <param name="discard_intron_redundant_transfrags" value="No" />\n+ <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" />\n+ <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" />\n+ <output file="gffcompare_out2.tracking" name="transcripts_tracking" />\n+ <output file="gffcompare_out2.gtf" name="transcripts_annotated" />\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+**GffCompare Overview**\n+\n+## GffCompare\n+* compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie).\n+* collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples)\n+* classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a\n+annotation file (also in GTF/GFF3 format)\n+\n+The original form of this program is also distributed as part of the Cufflinks suite, under the name "CuffCompare"\n+(see manual: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/). Most of the options and parameters of CuffCompare\n+are supported by GffCompare, while new features will likely be added to GffCompare in the future.\n+\n+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),\n+gffcompare switches into "annotation mode" and it generates a .annotated.gtf file instead of the .merged.gtf produced by CuffCompare with the\n+same parameters. This file has the same general format as CuffCompare\'s .merged.gtf file (with "class codes" assigned to transcripts as per\n+their relationship with the matching/overlapping reference transcript), but the original transcript IDs are preserved, so gffcompare can thus\n+be used as a simple way of annotating a set of transcripts.\n+\n+Another important difference is that the input transcripts are no longer discarded when they are found to be "intron redundant", i.e.\n+contained within other, longer isoforms. CuffCompare had the -G option to prevent collapsing of such intron redundant isoforms into\n+their longer "containers", but GffCompare has made this the default mode of operation (hence the -G option is no longer needed\n+and is simply ignored when given).\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1038/nbt.1621</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_in1.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_in1.gtf Fri Apr 07 16:02:07 2017 -0400 |
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| b'@@ -0,0 +1,100 @@\n+chr1\tCufflinks\ttranscript\t3111450\t3111490\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";\n+chr1\tCufflinks\texon\t3111450\t3111490\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";\n+chr1\tCufflinks\ttranscript\t3111546\t3111576\t1000\t.\t.\tgene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";\n+chr1\tCufflinks\texon\t3111546\t3111576\t1000\t.\t.\tgene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";\n+chr1\tCufflinks\ttranscript\t3200326\t3200352\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3200326\t3200352\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3200023\t3200191\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";\n+chr1\tCufflinks\texon\t3200023\t3200191\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";\n+chr1\tCufflinks\ttranscript\t3201078\t3201481\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+chr1\tCufflinks\texon\t3201078\t3201481\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+chr1\tCufflinks\ttranscript\t3201673\t3201699\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3201673\t3201699\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3204755\t3204833\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\texon\t3204755\t3204833\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\ttranscript\t3212214\t3212292\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\texon\t3212214\t3212292\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\ttranscript\t3213096\t3213192\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";\n+chr1\tCufflinks\texon\t3213096\t3213192\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";\n+chr1\tCufflinks\ttranscript\t3212368\t3212439\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";\n+chr1\tCufflinks\texon\t3212368\t3212439\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";\n+chr1\tCufflinks'..b'0000";\n+chr1\tCufflinks\ttranscript\t3363215\t3363278\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";\n+chr1\tCufflinks\texon\t3363215\t3363278\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";\n+chr1\tCufflinks\ttranscript\t3363754\t3363849\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr1\tCufflinks\texon\t3363754\t3363849\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr1\tCufflinks\ttranscript\t3367136\t3367162\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3367136\t3367162\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3367334\t3367382\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";\n+chr1\tCufflinks\texon\t3367334\t3367382\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";\n+chr1\tCufflinks\ttranscript\t3377212\t3377262\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";\n+chr1\tCufflinks\texon\t3377212\t3377262\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";\n+chr1\tCufflinks\ttranscript\t3391326\t3391352\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3391326\t3391352\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3435842\t3435880\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";\n+chr1\tCufflinks\texon\t3435842\t3435880\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";\n+chr1\tCufflinks\ttranscript\t3447762\t3447788\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr1\tCufflinks\texon\t3447762\t3447788\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr1\tCufflinks\ttranscript\t3450907\t3450965\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";\n+chr1\tCufflinks\texon\t3450907\t3450965\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";\n+chr1\tCufflinks\ttranscript\t3451052\t3451109\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";\n+chr1\tCufflinks\texon\t3451052\t3451109\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";\n' |
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| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_in2.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_in2.gtf Fri Apr 07 16:02:07 2017 -0400 |
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| b'@@ -0,0 +1,100 @@\n+chr1\tCufflinks\ttranscript\t3174766\t3174792\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3174766\t3174792\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3187402\t3187428\t1000\t.\t.\tgene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3187402\t3187428\t1000\t.\t.\tgene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3188522\t3188548\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672";\n+chr1\tCufflinks\texon\t3188522\t3188548\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672";\n+chr1\tCufflinks\ttranscript\t3190859\t3191434\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500";\n+chr1\tCufflinks\texon\t3190859\t3191434\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500";\n+chr1\tCufflinks\ttranscript\t3191513\t3192077\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341";\n+chr1\tCufflinks\texon\t3191513\t3192077\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "34.0729325807"; 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transcript_id "CUFF.19.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1'..b'760563";\n+chr1\tCufflinks\ttranscript\t3355908\t3356119\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792";\n+chr1\tCufflinks\texon\t3355908\t3356119\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792";\n+chr1\tCufflinks\ttranscript\t3356181\t3356225\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000";\n+chr1\tCufflinks\texon\t3356181\t3356225\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000";\n+chr1\tCufflinks\ttranscript\t3363077\t3363176\t1000\t.\t.\tgene_id "CUFF.85"; 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transcript_id "CUFF.89.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500";\n+chr1\tCufflinks\ttranscript\t3367211\t3367237\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3367211\t3367237\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3369581\t3369607\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3369581\t3369607\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3375002\t3375028\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3375002\t3375028\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3379889\t3379915\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3379889\t3379915\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3386740\t3386836\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402";\n+chr1\tCufflinks\texon\t3386740\t3386836\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402";\n' |
| b |
| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_in3.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_in3.gtf Fri Apr 07 16:02:07 2017 -0400 |
| b |
| b'@@ -0,0 +1,100 @@\n+chr1\tmm9_refFlat\tstop_codon\t3206103\t3206105\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\tCDS\t3206106\t3207049\t0.000000\t-\t2\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\texon\t3204563\t3207049\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\tCDS\t3411783\t3411982\t0.000000\t-\t1\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\texon\t3411783\t3411982\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\tCDS\t3660633\t3661429\t0.000000\t-\t0\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\tstart_codon\t3661427\t3661429\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\texon\t3660633\t3661579\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\tstop_codon\t4334681\t4334683\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\tCDS\t4334684\t4340172\t0.000000\t-\t2\tgene_id "Rp1"; 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transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t4827082\t4827155\t0.000000\t+\t2\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4827082\t4827155\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t4829468\t4829569\t0.000000\t+\t0\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4829468\t4829569\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t4831037\t4831213\t0.000000\t+\t0\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4831037\t4831213\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t4835044\t4835094\t0.000000\t+\t0\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tstop_codon\t4835095\t4835097\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4835044\t4836816\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tstart_codon\t4847995\t4847997\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4847995\t4848057\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4847775\t4848057\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4857551\t4857613\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4857551\t4857613\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4868108\t4868213\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4868108\t4868213\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4876825\t4876912\t0.000000\t+\t2\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4876825\t4876912\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4879538\t4879683\t0.000000\t+\t1\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4879538\t4879683\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4880821\t4880877\t0.000000\t+\t2\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4880821\t4880877\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4881996\t4882150\t0.000000\t+\t2\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4881996\t4882150\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4883498\t4883644\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4883498\t4883644\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4885015\t4885086\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4885015\t4885086\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4886437\t4886442\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tstop_codon\t4886443\t4886445\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4886437\t4887987\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tstart_codon\t4847995\t4847997\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n+chr1\tmm9_refFlat\tCDS\t4847995\t4848057\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n+chr1\tmm9_refFlat\texon\t4847775\t4848057\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n+chr1\tmm9_refFlat\tCDS\t4857551\t4857613\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n' |
| b |
| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_in4.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_in4.gtf Fri Apr 07 16:02:07 2017 -0400 |
| b |
| b'@@ -0,0 +1,208 @@\n+# stringtie --merge -p 1 -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /galaxy-repl/main/files/019/441/dataset_19441936.dat /galaxy-repl/main/files/018/604/dataset_18604623.dat /galaxy-repl/main/files/018/604/dataset_18604626.dat /galaxy-repl/main/files/018/604/dataset_18604628.dat /galaxy-repl/main/files/018/604/dataset_18604631.dat\n+# StringTie version 1.2.3\n+chr1\tStringTie\ttranscript\t29485012\t29485458\t1000\t-\t.\tgene_id "MSTRG.1"; transcript_id "MSTRG.1.1";\n+chr1\tStringTie\texon\t29485012\t29485458\t1000\t-\t.\tgene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1";\n+chr1\tStringTie\ttranscript\t86909344\t86909692\t1000\t-\t.\tgene_id "MSTRG.2"; transcript_id "MSTRG.2.1";\n+chr1\tStringTie\texon\t86909344\t86909692\t1000\t-\t.\tgene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1";\n+chr1\tStringTie\ttranscript\t160930303\t160940234\t1000\t+\t.\tgene_id "MSTRG.3"; transcript_id "MSTRG.3.1";\n+chr1\tStringTie\texon\t160930303\t160930344\t1000\t+\t.\tgene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1";\n+chr1\tStringTie\texon\t160938112\t160938232\t1000\t+\t.\tgene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "2";\n+chr1\tStringTie\texon\t160939995\t160940234\t1000\t+\t.\tgene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "3";\n+chr1\tStringTie\ttranscript\t160940817\t160967997\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1";\n+chr1\tStringTie\texon\t160940817\t160940994\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "1";\n+chr1\tStringTie\texon\t160942528\t160942728\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "2";\n+chr1\tStringTie\texon\t160946534\t160946666\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "3";\n+chr1\tStringTie\texon\t160948307\t160948425\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "4";\n+chr1\tStringTie\texon\t160950222\t160950334\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "5";\n+chr1\tStringTie\texon\t160950841\t160951122\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "6";\n+chr1\tStringTie\texon\t160951615\t160951829\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "7";\n+chr1\tStringTie\texon\t160954784\t160955151\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "8";\n+chr1\tStringTie\texon\t160955815\t160955979\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "9";\n+chr1\tStringTie\texon\t160959401\t160959553\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "10";\n+chr1\tStringTie\texon\t160962271\t160962484\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "11";\n+chr1\tStringTie\texon\t160963479\t160963569\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "12";\n+chr1\tStringTie\texon\t160963708\t160963840\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "13";\n+chr1\tStringTie\texon\t160964950\t160965120\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "14";\n+chr1\tStringTie\texon\t160965673\t160965788\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "15";\n+chr1\tStringTie\texon\t160967647\t160967997\t1000\t+\t.\tgene_id "MSTRG.4"; transcript_id "MSTRG.4.1"; exon_number "16";\n+chr1\tStringTie\ttranscript\t160968644\t160972020\t1000\t+\t.\tgene_id "MSTRG.5"; transcript_id "MSTRG.5.1";\n+chr1\tStringTie\texon\t160968644\t160972020\t1000\t+\t.\tgene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1";\n+chr1\tStringTie\ttranscript\t160972938\t160974977\t1000\t+\t.\tgene_id "MSTRG.6"; transcript_id "MSTRG.6.1";\n+chr1\tStringTie\texon\t160972938\t160974977\t1000\t+\t.\tgene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161003085\t161003516\t1000\t+\t.\tgene_id "MSTRG.7"; transcript_id "MSTRG.7.1";\n+chr1\tStringTie\texon\t161003085\t161003516\t1000\t+\t.\tgene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161003658\t161004769\t1000\t-\t.\tgene_id "MSTRG.8"; transcript_id "MSTRG.8.1";\n+chr1\tStringTie\texon\t161003658\t161004769\t1000\t-\t.\tgene_id "MSTRG.8"; transcript_id "MSTRG.8.1'..b'.23"; transcript_id "MSTRG.23.1";\n+chr1\tStringTie\texon\t161085014\t161086329\t1000\t+\t.\tgene_id "MSTRG.23"; transcript_id "MSTRG.23.1"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161088497\t161088913\t1000\t+\t.\tgene_id "MSTRG.24"; transcript_id "MSTRG.24.1";\n+chr1\tStringTie\texon\t161088497\t161088913\t1000\t+\t.\tgene_id "MSTRG.24"; transcript_id "MSTRG.24.1"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161088915\t161090275\t1000\t-\t.\tgene_id "MSTRG.25"; transcript_id "MSTRG.25.1";\n+chr1\tStringTie\texon\t161088915\t161090275\t1000\t-\t.\tgene_id "MSTRG.25"; transcript_id "MSTRG.25.1"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161089415\t161131512\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1";\n+chr1\tStringTie\texon\t161089415\t161090511\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "1";\n+chr1\tStringTie\texon\t161093681\t161093787\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "2";\n+chr1\tStringTie\texon\t161095529\t161095737\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "3";\n+chr1\tStringTie\texon\t161098263\t161098396\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "4";\n+chr1\tStringTie\texon\t161099142\t161099285\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "5";\n+chr1\tStringTie\texon\t161101451\t161101634\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "6";\n+chr1\tStringTie\texon\t161102979\t161103094\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "7";\n+chr1\tStringTie\texon\t161105401\t161105495\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "8";\n+chr1\tStringTie\texon\t161106707\t161106865\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "9";\n+chr1\tStringTie\texon\t161109222\t161109795\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "10";\n+chr1\tStringTie\texon\t161130389\t161130452\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "11";\n+chr1\tStringTie\texon\t161131363\t161131512\t1000\t+\t.\tgene_id "MSTRG.26"; transcript_id "MSTRG.26.1"; exon_number "12";\n+chr1\tStringTie\ttranscript\t161090412\t161131492\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1";\n+chr1\tStringTie\texon\t161090412\t161090511\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "1";\n+chr1\tStringTie\texon\t161093681\t161093787\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "2";\n+chr1\tStringTie\texon\t161095529\t161095737\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "3";\n+chr1\tStringTie\texon\t161098263\t161098396\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "4";\n+chr1\tStringTie\texon\t161099142\t161099285\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "5";\n+chr1\tStringTie\texon\t161101451\t161101634\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "6";\n+chr1\tStringTie\texon\t161102979\t161103094\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "7";\n+chr1\tStringTie\texon\t161105401\t161105495\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "8";\n+chr1\tStringTie\texon\t161106707\t161106865\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "9";\n+chr1\tStringTie\texon\t161109222\t161109795\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "10";\n+chr1\tStringTie\texon\t161130389\t161130452\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "11";\n+chr1\tStringTie\texon\t161131363\t161131492\t1000\t-\t.\tgene_id "MSTRG.27"; transcript_id "MSTRG.27.1"; exon_number "12";\n+chr1\tStringTie\ttranscript\t161123665\t161123877\t1000\t+\t.\tgene_id "MSTRG.28"; transcript_id "MSTRG.28.1";\n+chr1\tStringTie\texon\t161123665\t161123877\t1000\t+\t.\tgene_id "MSTRG.28"; transcript_id "MSTRG.28.1"; exon_number "1";\n+chr1\tStringTie\ttranscript\t192074156\t192074378\t1000\t-\t.\tgene_id "MSTRG.29"; transcript_id "MSTRG.29.1";\n+chr1\tStringTie\texon\t192074156\t192074378\t1000\t-\t.\tgene_id "MSTRG.29"; transcript_id "MSTRG.29.1"; exon_number "1";\n' |
| b |
| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_in5.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_in5.gtf Fri Apr 07 16:02:07 2017 -0400 |
| b |
| b'@@ -0,0 +1,1395 @@\n+chr1\tmm10_knownGene\tCDS\t160930303\t160930344\t0.000000\t+\t0\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160930303\t160930344\t0.000000\t+\t0\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160930303\t160930344\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160930303\t160930344\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160938112\t160938232\t0.000000\t+\t0\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160938112\t160938232\t0.000000\t+\t0\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160938112\t160938232\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160938112\t160938232\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160939995\t160940234\t0.000000\t+\t2\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160939995\t160940234\t0.000000\t+\t2\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160939995\t160940234\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160939995\t160940234\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160940819\t160940994\t0.000000\t+\t2\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160940819\t160940994\t0.000000\t+\t2\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160940819\t160940994\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160940819\t160940994\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160942528\t160942728\t0.000000\t+\t0\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160942528\t160942728\t0.000000\t+\t0\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160942528\t160942728\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160942528\t160942728\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160946534\t160946666\t0.000000\t+\t0\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160946534\t160946666\t0.000000\t+\t0\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160946534\t160946666\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160946534\t160946666\t0.000000\t+\t.\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160948307\t160948425\t0.000000\t+\t2\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\tCDS\t160948307\t160948425\t0.000000\t+\t2\tgene_id "uc007del.2"; transcript_id "uc007del.2"; \n+chr1\tmm10_knownGene\texon\t160948307\t160948425\t0.000000\t+\t.\tgene_id "uc007del.2"; 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| b |
| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_out1.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out1.gtf Fri Apr 07 16:02:07 2017 -0400 |
| b |
| b'@@ -0,0 +1,196 @@\n+chr1\tCufflinks\ttranscript\t3204755\t3204833\t.\t-\t.\ttranscript_id "TCONS_00000001"; gene_id "XLOC_000001"; gene_name "Xkr4"; oId "CUFF.13.1"; cmp_ref "Xkr4"; class_code "c"; tss_id "TSS1";\n+chr1\tCufflinks\texon\t3204755\t3204833\t.\t-\t.\ttranscript_id "TCONS_00000001"; gene_id "XLOC_000001"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3111450\t3111490\t.\t.\t.\ttranscript_id "TCONS_00000002"; gene_id "XLOC_000002"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2";\n+chr1\tCufflinks\texon\t3111450\t3111490\t.\t.\t.\ttranscript_id "TCONS_00000002"; gene_id "XLOC_000002"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3111546\t3111576\t.\t.\t.\ttranscript_id "TCONS_00000003"; gene_id "XLOC_000003"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3";\n+chr1\tCufflinks\texon\t3111546\t3111576\t.\t.\t.\ttranscript_id "TCONS_00000003"; gene_id "XLOC_000003"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3174766\t3174792\t.\t.\t.\ttranscript_id "TCONS_00000051"; gene_id "XLOC_000004"; 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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\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+chr1\tCufflinks\texon\t3435842\t3435880\t.\t.\t.\ttranscript_id "TCONS_00000047"; gene_id "XLOC_000084"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3447762\t3447788\t.\t.\t.\ttranscript_id "TCONS_00000048"; gene_id "XLOC_000085"; gene_name "Xkr4"; oId "CUFF.95.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS91";\n+chr1\tCufflinks\texon\t3447762\t3447788\t.\t.\t.\ttranscript_id "TCONS_00000048"; gene_id "XLOC_000085"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3450907\t3450965\t.\t.\t.\ttranscript_id "TCONS_00000049"; gene_id "XLOC_000086"; gene_name "Xkr4"; oId "CUFF.97.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS92";\n+chr1\tCufflinks\texon\t3450907\t3450965\t.\t.\t.\ttranscript_id "TCONS_00000049"; gene_id "XLOC_000086"; exon_number "1";\n+chr1\tCufflinks\ttranscript\t3451052\t3451109\t.\t.\t.\ttranscript_id "TCONS_00000050"; gene_id "XLOC_000087"; gene_name "Xkr4"; oId "CUFF.99.1"; cmp_ref "Xkr4"; class_code "i"; tss_id "TSS93";\n+chr1\tCufflinks\texon\t3451052\t3451109\t.\t.\t.\ttranscript_id "TCONS_00000050"; gene_id "XLOC_000087"; exon_number "1";\n' |
| b |
| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_out1.loci --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out1.loci Fri Apr 07 16:02:07 2017 -0400 |
| [ |
| @@ -0,0 +1,87 @@ +XLOC_000001 chr1[-]3204563-3661579 Xkr4|Xkr4 CUFF.13.1 - +XLOC_000002 chr1[.]3111450-3111490 - CUFF.1.1 - +XLOC_000003 chr1[.]3111546-3111576 - CUFF.3.1 - +XLOC_000004 chr1[.]3174766-3174792 - - CUFF.1.1 +XLOC_000005 chr1[.]3187402-3187428 - - CUFF.3.1 +XLOC_000006 chr1[.]3188522-3188548 - - CUFF.5.1 +XLOC_000007 chr1[.]3189811-3190789 - CUFF.29.1,CUFF.31.1,CUFF.33.1 CUFF.11.1 +XLOC_000008 chr1[.]3190859-3191434 - - CUFF.7.1 +XLOC_000009 chr1[.]3191513-3192077 - CUFF.35.1,CUFF.37.1 CUFF.9.1 +XLOC_000010 chr1[.]3192251-3192336 - - CUFF.13.1 +XLOC_000011 chr1[.]3192442-3192494 - CUFF.39.1 - +XLOC_000012 chr1[.]3192551-3192629 - CUFF.41.1 - +XLOC_000013 chr1[.]3192650-3192676 - - CUFF.15.1 +XLOC_000014 chr1[.]3192732-3192811 - CUFF.43.1 - +XLOC_000015 chr1[.]3192941-3193042 - CUFF.45.1 - +XLOC_000016 chr1[.]3194186-3194226 - CUFF.47.1 - +XLOC_000017 chr1[.]3194303-3194329 - CUFF.49.1 - +XLOC_000018 chr1[.]3194707-3194733 - - CUFF.17.1 +XLOC_000019 chr1[.]3195084-3195110 - CUFF.51.1 - +XLOC_000020 chr1[.]3195451-3195477 - CUFF.53.1 - +XLOC_000021 chr1[.]3197090-3197116 - CUFF.55.1 - +XLOC_000022 chr1[.]3197247-3197273 - CUFF.57.1 - +XLOC_000023 chr1[.]3197347-3197373 - CUFF.59.1 - +XLOC_000024 chr1[.]3197426-3197452 - - CUFF.19.1 +XLOC_000025 chr1[.]3200023-3200191 - CUFF.7.1 CUFF.23.1 +XLOC_000026 chr1[.]3200326-3200352 - CUFF.5.1 - +XLOC_000027 chr1[.]3200431-3200457 - - CUFF.21.1 +XLOC_000028 chr1[.]3201008-3201039 - - CUFF.26.1 +XLOC_000029 chr1[.]3201078-3201481 - CUFF.9.1 CUFF.25.1 +XLOC_000030 chr1[.]3201597-3201666 - - CUFF.29.1 +XLOC_000031 chr1[.]3201673-3201699 - CUFF.11.1 - +XLOC_000032 chr1[.]3201726-3201809 - - CUFF.31.1 +XLOC_000033 chr1[.]3211522-3211561 - - CUFF.33.1 +XLOC_000034 chr1[.]3212214-3212292 - CUFF.15.1 - +XLOC_000035 chr1[.]3212368-3212439 - CUFF.19.1 - +XLOC_000036 chr1[.]3212718-3212801 - - CUFF.35.1 +XLOC_000037 chr1[.]3213096-3213242 - CUFF.17.1 CUFF.37.1 +XLOC_000038 chr1[.]3240607-3240633 - - CUFF.39.1 +XLOC_000039 chr1[.]3242480-3242512 - - CUFF.41.1 +XLOC_000040 chr1[.]3242634-3242923 - CUFF.25.1 - +XLOC_000041 chr1[.]3242925-3243005 - - CUFF.43.1 +XLOC_000042 chr1[.]3243019-3243079 - CUFF.21.1 - +XLOC_000043 chr1[.]3243109-3243154 - - CUFF.45.1 +XLOC_000044 chr1[.]3243348-3243401 - CUFF.23.1 - +XLOC_000045 chr1[.]3254080-3254106 - - CUFF.47.1 +XLOC_000046 chr1[.]3256975-3257011 - CUFF.27.1 - +XLOC_000047 chr1[.]3277156-3277182 - - CUFF.49.1 +XLOC_000048 chr1[.]3277191-3277218 - CUFF.61.1 - +XLOC_000049 chr1[.]3277914-3278390 - CUFF.63.1 CUFF.51.1 +XLOC_000050 chr1[.]3280118-3280144 - - CUFF.53.1 +XLOC_000051 chr1[.]3280499-3280525 - - CUFF.55.1 +XLOC_000052 chr1[.]3280687-3280741 - CUFF.65.1 - +XLOC_000053 chr1[.]3282505-3282531 - - CUFF.57.1 +XLOC_000054 chr1[.]3282651-3282677 - - CUFF.59.1 +XLOC_000055 chr1[.]3282761-3282832 - - CUFF.61.1 +XLOC_000056 chr1[.]3284967-3284993 - - CUFF.63.1 +XLOC_000057 chr1[.]3290489-3290553 - CUFF.67.1 - +XLOC_000058 chr1[.]3290799-3290859 - - CUFF.65.1 +XLOC_000059 chr1[.]3290920-3291273 - CUFF.69.1,CUFF.71.1 CUFF.69.1 +XLOC_000060 chr1[.]3299444-3299664 - CUFF.73.1 CUFF.67.1 +XLOC_000061 chr1[.]3299692-3299733 - - CUFF.71.1 +XLOC_000062 chr1[.]3300052-3300078 - CUFF.75.1 - +XLOC_000063 chr1[.]3307749-3307775 - - CUFF.73.1 +XLOC_000064 chr1[.]3318621-3318647 - - CUFF.75.1 +XLOC_000065 chr1[.]3319000-3319051 - CUFF.77.1 - +XLOC_000066 chr1[.]3330528-3330554 - - CUFF.77.1 +XLOC_000067 chr1[.]3351241-3351311 - - CUFF.79.1 +XLOC_000068 chr1[.]3355888-3356119 - CUFF.79.1 CUFF.81.1 +XLOC_000069 chr1[.]3356181-3356225 - - CUFF.83.1 +XLOC_000070 chr1[.]3363077-3363176 - - CUFF.85.1 +XLOC_000071 chr1[.]3363215-3363278 - CUFF.81.1 - +XLOC_000072 chr1[.]3363388-3363446 - - CUFF.87.1 +XLOC_000073 chr1[.]3363754-3363849 - CUFF.83.1 - +XLOC_000074 chr1[.]3364872-3364919 - - CUFF.89.1 +XLOC_000075 chr1[.]3367136-3367162 - CUFF.85.1 - +XLOC_000076 chr1[.]3367211-3367237 - - CUFF.91.1 +XLOC_000077 chr1[.]3367334-3367382 - CUFF.87.1 - +XLOC_000078 chr1[.]3369581-3369607 - - CUFF.93.1 +XLOC_000079 chr1[.]3375002-3375028 - - CUFF.95.1 +XLOC_000080 chr1[.]3377212-3377262 - CUFF.89.1 - +XLOC_000081 chr1[.]3379889-3379915 - - CUFF.97.1 +XLOC_000082 chr1[.]3386740-3386836 - - CUFF.99.1 +XLOC_000083 chr1[.]3391326-3391352 - CUFF.91.1 - +XLOC_000084 chr1[.]3435842-3435880 - CUFF.93.1 - +XLOC_000085 chr1[.]3447762-3447788 - CUFF.95.1 - +XLOC_000086 chr1[.]3450907-3450965 - CUFF.97.1 - +XLOC_000087 chr1[.]3451052-3451109 - CUFF.99.1 - |
| b |
| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_out1.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out1.stats Fri Apr 07 16:02:07 2017 -0400 |
| b |
| @@ -0,0 +1,34 @@ +# 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 +# + +#= Summary for dataset: /tmp/tmp9HJ0Pt/files/000/dataset_362.dat +# 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) +# Super-loci w/ reference transcripts: 1 +#-----------------| Sensitivity | Precision | + Base level: 2.2 | 2.3 | + Exon level: 0.0 | 0.0 | + Intron level: 0.0 | -nan | +Intron chain level: 0.0 | -nan | + Transcript level: 0.0 | 0.0 | + Locus level: 0.0 | 0.0 | + + Matching intron chains: 0 + Matching transcripts: 0 + Matching loci: 0 + + Missed exons: 2/3 ( 66.7%) + Novel exons: 49/50 ( 98.0%) + Missed introns: 2/2 (100.0%) + Missed loci: 0/1 ( 0.0%) + Novel loci: 49/50 ( 98.0%) + +#= Summary for dataset: /tmp/tmp9HJ0Pt/files/000/dataset_363.dat +# 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) |
| b |
| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_out1.tracking --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out1.tracking Fri Apr 07 16:02:07 2017 -0400 |
| b |
| b'@@ -0,0 +1,98 @@\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|3'..b'UFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000062\tXLOC_000028\t-\tu\t-\tq2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|-\n+TCONS_00000063\tXLOC_000030\t-\tu\t-\tq2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|-\n+TCONS_00000064\tXLOC_000032\t-\tu\t-\tq2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|-\n+TCONS_00000065\tXLOC_000033\tXkr4|Xkr4\ti\t-\tq2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|-\n+TCONS_00000066\tXLOC_000036\tXkr4|Xkr4\ti\t-\tq2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|-\n+TCONS_00000067\tXLOC_000037\tXkr4|Xkr4\ti\t-\tq2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|-\n+TCONS_00000068\tXLOC_000038\tXkr4|Xkr4\ti\t-\tq2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|-\n+TCONS_00000069\tXLOC_000039\tXkr4|Xkr4\ti\t-\tq2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|-\n+TCONS_00000070\tXLOC_000041\tXkr4|Xkr4\ti\t-\tq2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|-\n+TCONS_00000071\tXLOC_000043\tXkr4|Xkr4\ti\t-\tq2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|-\n+TCONS_00000072\tXLOC_000045\tXkr4|Xkr4\ti\t-\tq2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000073\tXLOC_000047\tXkr4|Xkr4\ti\t-\tq2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000074\tXLOC_000049\tXkr4|Xkr4\ti\t-\tq2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|-\n+TCONS_00000075\tXLOC_000050\tXkr4|Xkr4\ti\t-\tq2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|-\n+TCONS_00000076\tXLOC_000051\tXkr4|Xkr4\ti\t-\tq2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000077\tXLOC_000053\tXkr4|Xkr4\ti\t-\tq2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000078\tXLOC_000054\tXkr4|Xkr4\ti\t-\tq2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000079\tXLOC_000055\tXkr4|Xkr4\ti\t-\tq2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|-\n+TCONS_00000080\tXLOC_000056\tXkr4|Xkr4\ti\t-\tq2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000081\tXLOC_000058\tXkr4|Xkr4\ti\t-\tq2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|-\n+TCONS_00000082\tXLOC_000059\tXkr4|Xkr4\ti\t-\tq2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|-\n+TCONS_00000083\tXLOC_000060\tXkr4|Xkr4\ti\t-\tq2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|-\n+TCONS_00000084\tXLOC_000061\tXkr4|Xkr4\ti\t-\tq2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|-\n+TCONS_00000085\tXLOC_000063\tXkr4|Xkr4\ti\t-\tq2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000086\tXLOC_000064\tXkr4|Xkr4\ti\t-\tq2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|-\n+TCONS_00000087\tXLOC_000066\tXkr4|Xkr4\ti\t-\tq2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|-\n+TCONS_00000088\tXLOC_000067\tXkr4|Xkr4\ti\t-\tq2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|-\n+TCONS_00000089\tXLOC_000068\tXkr4|Xkr4\ti\t-\tq2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|-\n+TCONS_00000090\tXLOC_000069\tXkr4|Xkr4\ti\t-\tq2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|-\n+TCONS_00000091\tXLOC_000070\tXkr4|Xkr4\ti\t-\tq2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|-\n+TCONS_00000092\tXLOC_000072\tXkr4|Xkr4\ti\t-\tq2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|-\n+TCONS_00000093\tXLOC_000074\tXkr4|Xkr4\ti\t-\tq2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|-\n+TCONS_00000094\tXLOC_000076\tXkr4|Xkr4\ti\t-\tq2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000095\tXLOC_000078\tXkr4|Xkr4\ti\t-\tq2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000096\tXLOC_000079\tXkr4|Xkr4\ti\t-\tq2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000097\tXLOC_000081\tXkr4|Xkr4\ti\t-\tq2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000098\tXLOC_000082\tXkr4|Xkr4\ti\t-\tq2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|-\n' |
| b |
| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_out2.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2.gtf Fri Apr 07 16:02:07 2017 -0400 |
| b |
| b'@@ -0,0 +1,206 @@\n+chr1\tStringTie\ttranscript\t160930303\t160940234\t.\t+\t.\ttranscript_id "MSTRG.3.1"; gene_id "MSTRG.3"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS1";\n+chr1\tStringTie\texon\t160930303\t160930344\t.\t+\t.\ttranscript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "1";\n+chr1\tStringTie\texon\t160938112\t160938232\t.\t+\t.\ttranscript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "2";\n+chr1\tStringTie\texon\t160939995\t160940234\t.\t+\t.\ttranscript_id "MSTRG.3.1"; gene_id "MSTRG.3"; exon_number "3";\n+chr1\tStringTie\ttranscript\t160940817\t160967997\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS2";\n+chr1\tStringTie\texon\t160940817\t160940994\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "1";\n+chr1\tStringTie\texon\t160942528\t160942728\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "2";\n+chr1\tStringTie\texon\t160946534\t160946666\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "3";\n+chr1\tStringTie\texon\t160948307\t160948425\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "4";\n+chr1\tStringTie\texon\t160950222\t160950334\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "5";\n+chr1\tStringTie\texon\t160950841\t160951122\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "6";\n+chr1\tStringTie\texon\t160951615\t160951829\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "7";\n+chr1\tStringTie\texon\t160954784\t160955151\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "8";\n+chr1\tStringTie\texon\t160955815\t160955979\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "9";\n+chr1\tStringTie\texon\t160959401\t160959553\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "10";\n+chr1\tStringTie\texon\t160962271\t160962484\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "11";\n+chr1\tStringTie\texon\t160963479\t160963569\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "12";\n+chr1\tStringTie\texon\t160963708\t160963840\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "13";\n+chr1\tStringTie\texon\t160964950\t160965120\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "14";\n+chr1\tStringTie\texon\t160965673\t160965788\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "15";\n+chr1\tStringTie\texon\t160967647\t160967997\t.\t+\t.\ttranscript_id "MSTRG.4.1"; gene_id "MSTRG.4"; exon_number "16";\n+chr1\tStringTie\ttranscript\t160968644\t160972020\t.\t+\t.\ttranscript_id "MSTRG.5.1"; gene_id "MSTRG.5"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS3";\n+chr1\tStringTie\texon\t160968644\t160972020\t.\t+\t.\ttranscript_id "MSTRG.5.1"; gene_id "MSTRG.5"; exon_number "1";\n+chr1\tStringTie\ttranscript\t160972938\t160974977\t.\t+\t.\ttranscript_id "MSTRG.6.1"; gene_id "MSTRG.6"; gene_name "uc007del.2"; xloc "XLOC_000001"; cmp_ref "uc007del.2"; class_code "c"; tss_id "TSS4";\n+chr1\tStringTie\texon\t160972938\t160974977\t.\t+\t.\ttranscript_id "MSTRG.6.1"; gene_id "MSTRG.6"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161003085\t161003516\t.\t+\t.\ttranscript_id "MSTRG.7.1"; gene_id "MSTRG.7"; xloc "XLOC_000002"; class_code "u"; tss_id "TSS5";\n+chr1\tStringTie\texon\t161003085\t161003516\t.\t+\t.\ttranscript_id "MSTRG.7.1"; gene_id "MSTRG.7"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161006151\t161006466\t.\t+\t.\ttranscript_id "MSTRG.10.1"; gene_id "MSTRG.10"; xloc "XLOC_000003"; class_code "u"; tss_id "TSS6";\n+chr1\tStringTie\texon\t161006151\t161006466\t.\t+\t.\ttranscript_id "MSTRG.10.1"; gene_id "MSTRG.10"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161008375\t161008625\t.\t+\t.\ttranscript_id "MSTRG.12.1"; gene_id "MSTRG.12"; xloc "XLOC_000004"; class_code "u"; tss_id "TSS7";\n+chr1\tStringTie\texon\t161008375\t161008625\t.\t+\t.\ttranscript_id "MSTRG.12.1"; gene_id "MSTRG.12"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161009768\t161010195\t.\t+\t.\ttranscript_id "MSTRG.13.1"; gene_id "MS'..b'\tStringTie\texon\t161062782\t161062877\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "7";\n+chr1\tStringTie\texon\t161063247\t161063348\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "8";\n+chr1\tStringTie\texon\t161065225\t161065291\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "9";\n+chr1\tStringTie\texon\t161069080\t161069179\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "10";\n+chr1\tStringTie\texon\t161069993\t161070504\t.\t-\t.\ttranscript_id "MSTRG.19.1"; gene_id "MSTRG.19"; exon_number "11";\n+chr1\tStringTie\ttranscript\t161051331\t161070649\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; gene_name "uc007dey.2"; xloc "XLOC_000019"; cmp_ref "uc007dey.2"; class_code "j"; tss_id "TSS30";\n+chr1\tStringTie\texon\t161051331\t161051438\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "1";\n+chr1\tStringTie\texon\t161056461\t161056530\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "2";\n+chr1\tStringTie\texon\t161057447\t161057553\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "3";\n+chr1\tStringTie\texon\t161060045\t161060091\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "4";\n+chr1\tStringTie\texon\t161060736\t161060859\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "5";\n+chr1\tStringTie\texon\t161062782\t161062877\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "6";\n+chr1\tStringTie\texon\t161063247\t161063348\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "7";\n+chr1\tStringTie\texon\t161065225\t161065291\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "8";\n+chr1\tStringTie\texon\t161069080\t161069179\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "9";\n+chr1\tStringTie\texon\t161069993\t161070649\t.\t-\t.\ttranscript_id "MSTRG.19.2"; gene_id "MSTRG.19"; exon_number "10";\n+chr1\tStringTie\ttranscript\t161088915\t161090275\t.\t-\t.\ttranscript_id "MSTRG.25.1"; gene_id "MSTRG.25"; gene_name "uc007dff.1"; xloc "XLOC_000020"; cmp_ref "uc007dff.1"; class_code "c"; tss_id "TSS31";\n+chr1\tStringTie\texon\t161088915\t161090275\t.\t-\t.\ttranscript_id "MSTRG.25.1"; gene_id "MSTRG.25"; exon_number "1";\n+chr1\tStringTie\ttranscript\t161090412\t161131492\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; gene_name "uc007dff.1"; xloc "XLOC_000020"; cmp_ref "uc007dff.1"; class_code "="; tss_id "TSS32";\n+chr1\tStringTie\texon\t161090412\t161090511\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "1";\n+chr1\tStringTie\texon\t161093681\t161093787\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "2";\n+chr1\tStringTie\texon\t161095529\t161095737\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "3";\n+chr1\tStringTie\texon\t161098263\t161098396\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "4";\n+chr1\tStringTie\texon\t161099142\t161099285\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "5";\n+chr1\tStringTie\texon\t161101451\t161101634\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "6";\n+chr1\tStringTie\texon\t161102979\t161103094\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "7";\n+chr1\tStringTie\texon\t161105401\t161105495\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "8";\n+chr1\tStringTie\texon\t161106707\t161106865\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "9";\n+chr1\tStringTie\texon\t161109222\t161109795\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "10";\n+chr1\tStringTie\texon\t161130389\t161130452\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "11";\n+chr1\tStringTie\texon\t161131363\t161131492\t.\t-\t.\ttranscript_id "MSTRG.27.1"; gene_id "MSTRG.27"; exon_number "12";\n+chr1\tStringTie\ttranscript\t192074156\t192074378\t.\t-\t.\ttranscript_id "MSTRG.29.1"; gene_id "MSTRG.29"; xloc "XLOC_000021"; class_code "u"; tss_id "TSS33";\n+chr1\tStringTie\texon\t192074156\t192074378\t.\t-\t.\ttranscript_id "MSTRG.29.1"; gene_id "MSTRG.29"; exon_number "1";\n' |
| b |
| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_out2.loci --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2.loci Fri Apr 07 16:02:07 2017 -0400 |
| [ |
| @@ -0,0 +1,21 @@ +XLOC_000001 chr1[+]160930303-160974977 uc007del.2|uc007del.2 MSTRG.4.1,MSTRG.5.1,MSTRG.6.1,MSTRG.3.1 +XLOC_000002 chr1[+]161003085-161003516 - MSTRG.7.1 +XLOC_000003 chr1[+]161006151-161006466 - MSTRG.10.1 +XLOC_000004 chr1[+]161008375-161008625 - MSTRG.12.1 +XLOC_000005 chr1[+]161009768-161010195 - MSTRG.13.1 +XLOC_000006 chr1[+]161019713-161019962 - MSTRG.14.1 +XLOC_000007 chr1[+]161034351-161038539 uc007det.1|uc007det.1,uc007deu.1|uc007deu.1,uc007dev.1|uc007dev.1,uc007dew.1|uc007dew.1,uc011wun.1|uc011wun.1,uc007dex.1|uc007dex.1 MSTRG.16.1,MSTRG.16.2,MSTRG.16.3,MSTRG.16.4,MSTRG.16.5 +XLOC_000008 chr1[+]161041562-161070639 - MSTRG.18.1,MSTRG.18.2 +XLOC_000009 chr1[+]161070945-161086329 uc007dfe.4|uc007dfe.4,uc007dfc.3|uc007dfc.3,uc007dfd.3|uc007dfd.3,uc056yep.1|uc056yep.1 MSTRG.20.1,MSTRG.21.1,MSTRG.22.1,MSTRG.23.1 +XLOC_000010 chr1[+]161088497-161088913 - MSTRG.24.1 +XLOC_000011 chr1[+]161089415-161131512 - MSTRG.26.1 +XLOC_000012 chr1[+]161123665-161123877 - MSTRG.28.1 +XLOC_000013 chr1[-]29485012-29485458 - MSTRG.1.1 +XLOC_000014 chr1[-]86909344-86909692 - MSTRG.2.1 +XLOC_000015 chr1[-]161003658-161004769 - MSTRG.8.1 +XLOC_000016 chr1[-]161005030-161005802 - MSTRG.9.1 +XLOC_000017 chr1[-]161007444-161007700 - MSTRG.11.1 +XLOC_000018 chr1[-]161019713-161034848 uc007der.1|uc007der.1,uc007des.1|uc007des.1 MSTRG.15.1 +XLOC_000019 chr1[-]161041525-161070649 uc007dey.2|uc007dey.2,uc007dez.2|uc007dez.2 MSTRG.17.1,MSTRG.19.1,MSTRG.19.2 +XLOC_000020 chr1[-]161088497-161131492 uc007dff.1|uc007dff.1,uc007dfg.1|uc007dfg.1,uc007dfh.1|uc007dfh.1,uc007dfi.1|uc007dfi.1 MSTRG.25.1,MSTRG.27.1 +XLOC_000021 chr1[-]192074156-192074378 - MSTRG.29.1 |
| b |
| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_out2.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2.stats Fri Apr 07 16:02:07 2017 -0400 |
| b |
| @@ -0,0 +1,29 @@ +# 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 +# + +#= Summary for dataset: /tmp/tmp6wAQh6/files/000/dataset_667.dat +# 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 | + Exon level: 80.0 | 55.7 | + Intron level: 81.2 | 64.4 | +Intron chain level: 10.5 | 13.3 | + Transcript level: 10.0 | 5.7 | + Locus level: 28.6 | 6.9 | + + Matching intron chains: 2 + Matching transcripts: 2 + Matching loci: 2 + + Missed exons: 3/85 ( 3.5%) + Novel exons: 46/122 ( 37.7%) + Missed introns: 11/69 ( 15.9%) + Novel introns: 28/87 ( 32.2%) + Missed loci: 0/7 ( 0.0%) + Novel loci: 15/29 ( 51.7%) + + Total union super-loci across all input datasets: 21 |
| b |
| diff -r 000000000000 -r 3c97c841a443 test-data/gffcompare_out2.tracking --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gffcompare_out2.tracking Fri Apr 07 16:02:07 2017 -0400 |
| b |
| @@ -0,0 +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|- |
| b |
| diff -r 000000000000 -r 3c97c841a443 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Fri Apr 07 16:02:07 2017 -0400 |
| b |
| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
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| diff -r 000000000000 -r 3c97c841a443 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Apr 07 16:02:07 2017 -0400 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Location of SAMTools indexed FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> |