| Previous changeset 0:e323c49b8bcc (2018-04-12) Next changeset 2:d30ecf96e4cd (2018-04-20) |
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Commit message:
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/feelnc2asko commit 35a0acc7d7337781f376517f0ef821d836fc4bb9 |
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modified:
feelnc2asko.pl test-data/completeAnnot.gff3 |
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| diff -r e323c49b8bcc -r af75f883cab4 feelnc2asko.pl --- a/feelnc2asko.pl Thu Apr 12 06:05:23 2018 -0400 +++ b/feelnc2asko.pl Thu Apr 12 10:51:05 2018 -0400 |
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| @@ -62,6 +62,7 @@ -seq_id => $feat->seq_id()); # $geneft->add_tag_value("feelnc_type", "lncRNA"); $genes{$gene}=$geneft; + $geneft->add_tag_value("ID", $gene); } if (exists($transcripts{$mrna})) { |
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| diff -r e323c49b8bcc -r af75f883cab4 test-data/completeAnnot.gff3 --- a/test-data/completeAnnot.gff3 Thu Apr 12 06:05:23 2018 -0400 +++ b/test-data/completeAnnot.gff3 Thu Apr 12 10:51:05 2018 -0400 |
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| @@ -265,31 +265,31 @@ GL349622 Gnomon mRNA 2270755 2281456 . + . ID=rna336;Parent=LOC100168508;Dbxref=GeneID:100168508,Genbank:XM_008189547.2;Name=XM_008189547.2;feelnc_type=standard;gbkey=mRNA;gene=LOC100168508;model_evidence=Supporting evidence includes similarity to: 11 ESTs%2C 6 Proteins%2C and 100%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 7 samples with support for all annotated introns;product=ATPase family AAA domain-containing protein 3;transcript_id=XM_008189547.2 GL349622 Gnomon gene 2282156 2284359 . - . ID=LOC100165058;Dbxref=APHIDBASE:ACYPI006028,GeneID:100165058;Name=LOC100165058;feelnc_type=standard;gbkey=Gene;gene=LOC100165058;gene_biotype=protein_coding GL349622 Gnomon mRNA 2282156 2284359 . - . ID=rna337;Parent=LOC100165058;Dbxref=GeneID:100165058,Genbank:XM_001950091.4,APHIDBASE:ACYPI006028;Name=XM_001950091.4;feelnc_type=standard;gbkey=mRNA;gene=LOC100165058;model_evidence=Supporting evidence includes similarity to: 1 mRNA%2C 25 ESTs%2C 5 Proteins%2C and 99%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 44 samples with support for all annotated introns;product=solute carrier family 35 member B1;transcript_id=XM_001950091.4 -GL349622 Cufflinks gene 218384 219722 . - 1 -GL349622 Cufflinks mRNA 218384 219722 . - 1 ID=CUFF.77.1;Parent=CUFF.77;feelnc_type=lncRNA -GL349622 Cufflinks gene 604709 609482 . - 1 -GL349622 Cufflinks mRNA 604709 609482 . - 1 ID=CUFF.110.1;Parent=CUFF.110;feelnc_type=lncRNA -GL349622 Cufflinks gene 490324 536159 . - 1 -GL349622 Cufflinks mRNA 490324 536159 . - 1 ID=CUFF.85.1;Parent=CUFF.85;feelnc_type=lncRNA -GL349622 Cufflinks gene 2021789 2026165 . - 1 -GL349622 Cufflinks mRNA 2021789 2026165 . - 1 ID=CUFF.135.2;Parent=CUFF.135;feelnc_type=lncRNA -GL349622 Cufflinks gene 407420 409348 . + 1 ID=CUFF.82 -GL349622 Cufflinks mRNA 407420 409348 . + 1 ID=CUFF.82.1;Parent=CUFF.82;feelnc_type=new -GL349622 Cufflinks gene 490324 536159 . - 1 -GL349622 Cufflinks mRNA 533485 536159 . - 1 ID=CUFF.85.2;Parent=CUFF.85;feelnc_type=lncRNA +GL349622 Cufflinks gene 2021789 2026165 . - 1 ID=CUFF.135 +GL349622 Cufflinks mRNA 2021789 2024477 . - 1 ID=CUFF.135.1;Parent=CUFF.135;feelnc_type=new GL349622 Cufflinks gene 1722435 1724318 . + 1 ID=CUFF.130 GL349622 Cufflinks mRNA 1722435 1724318 . + 1 ID=CUFF.130.1;Parent=CUFF.130;feelnc_type=new -GL349622 Cufflinks gene 1200950 1218393 . + 1 ID=CUFF.289 -GL349622 Cufflinks mRNA 1200950 1218393 . + 1 ID=CUFF.289.1;Parent=CUFF.289;feelnc_type=new +GL349622 Cufflinks gene 1359442 1360152 . - 1 ID=CUFF.491 +GL349622 Cufflinks mRNA 1359442 1360152 . - 1 ID=CUFF.491.1;Parent=CUFF.491;feelnc_type=lncRNA GL349622 Cufflinks gene 1758962 1760807 . + 1 ID=CUFF.164 GL349622 Cufflinks mRNA 1758962 1760807 . + 1 ID=CUFF.164.1;Parent=CUFF.164;feelnc_type=new -GL349622 Cufflinks gene 1359442 1360152 . - 1 -GL349622 Cufflinks mRNA 1359442 1360152 . - 1 ID=CUFF.491.1;Parent=CUFF.491;feelnc_type=lncRNA +GL349622 Cufflinks gene 604709 609482 . - 1 ID=CUFF.110 +GL349622 Cufflinks mRNA 604709 609482 . - 1 ID=CUFF.110.1;Parent=CUFF.110;feelnc_type=lncRNA +GL349622 Cufflinks gene 490324 536159 . - 1 ID=CUFF.85 +GL349622 Cufflinks mRNA 490324 536159 . - 1 ID=CUFF.85.1;Parent=CUFF.85;feelnc_type=lncRNA +GL349622 Cufflinks gene 1160606 1161032 . - 1 ID=CUFF.350 +GL349622 Cufflinks mRNA 1160606 1161032 . - 1 ID=CUFF.350.1;Parent=CUFF.350;feelnc_type=lncRNA +GL349622 Cufflinks gene 1200950 1218393 . + 1 ID=CUFF.289 +GL349622 Cufflinks mRNA 1200950 1218393 . + 1 ID=CUFF.289.1;Parent=CUFF.289;feelnc_type=new +GL349622 Cufflinks gene 490324 536159 . - 1 ID=CUFF.85 +GL349622 Cufflinks mRNA 533485 536159 . - 1 ID=CUFF.85.2;Parent=CUFF.85;feelnc_type=lncRNA +GL349622 Cufflinks gene 407420 409348 . + 1 ID=CUFF.82 +GL349622 Cufflinks mRNA 407420 409348 . + 1 ID=CUFF.82.1;Parent=CUFF.82;feelnc_type=new +GL349622 Cufflinks gene 218384 219722 . - 1 ID=CUFF.77 +GL349622 Cufflinks mRNA 218384 219722 . - 1 ID=CUFF.77.1;Parent=CUFF.77;feelnc_type=lncRNA +GL349622 Cufflinks gene 400758 405243 . - 1 ID=CUFF.80 +GL349622 Cufflinks mRNA 400758 405243 . - 1 ID=CUFF.80.1;Parent=CUFF.80;feelnc_type=lncRNA +GL349622 Cufflinks gene 2021789 2026165 . - 1 ID=CUFF.135 +GL349622 Cufflinks mRNA 2021789 2026165 . - 1 ID=CUFF.135.2;Parent=CUFF.135;feelnc_type=lncRNA GL349622 Cufflinks gene 675392 678724 . + 1 ID=CUFF.91 GL349622 Cufflinks mRNA 675392 678724 . + 1 ID=CUFF.91.1;Parent=CUFF.91;feelnc_type=new -GL349622 Cufflinks gene 2021789 2026165 . - 1 -GL349622 Cufflinks mRNA 2021789 2024477 . - 1 ID=CUFF.135.1;Parent=CUFF.135;feelnc_type=new -GL349622 Cufflinks gene 400758 405243 . - 1 -GL349622 Cufflinks mRNA 400758 405243 . - 1 ID=CUFF.80.1;Parent=CUFF.80;feelnc_type=lncRNA -GL349622 Cufflinks gene 1160606 1161032 . - 1 -GL349622 Cufflinks mRNA 1160606 1161032 . - 1 ID=CUFF.350.1;Parent=CUFF.350;feelnc_type=lncRNA |