| Previous changeset 1:a07680f3033a (2017-03-07) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 651fae48371f845578753052c6fe173e3bb35670 |
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modified:
ensembl_longest_cds_per_gene.py ensembl_longest_cds_per_gene.xml test-data/Mus_musculus.GRCm38.cds.longest.fa |
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| diff -r a07680f3033a -r 6cf9f7f6509c ensembl_longest_cds_per_gene.py --- a/ensembl_longest_cds_per_gene.py Tue Mar 07 11:12:55 2017 -0500 +++ b/ensembl_longest_cds_per_gene.py Wed Mar 15 20:23:13 2017 -0400 |
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| @@ -1,7 +1,6 @@ """ This script reads a CDS FASTA file from Ensembl and outputs a FASTA file with -only the longest CDS sequence for each gene. The header of the sequences in the -output file will be the transcript id without version. +only the longest CDS sequence for each gene. """ from __future__ import print_function @@ -33,7 +32,10 @@ """ Remove the optional '.VERSION' from an Ensembl id. """ - return s.split('.')[0] + if s.startswith('ENS'): + return s.split('.')[0] + else: + return s parser = optparse.OptionParser() @@ -52,7 +54,6 @@ for entry in FASTAReader_gen(options.input_fasta_filename): transcript_id, rest = entry.header[1:].split(' ', 1) - transcript_id = remove_id_version(transcript_id) gene_id = None for s in rest.split(' '): if s.startswith('gene:'): @@ -73,6 +74,6 @@ with open(options.output_fasta_filename, 'w') as output_fasta_file: for entry in FASTAReader_gen(options.input_fasta_filename): - transcript_id = remove_id_version(entry.header[1:].split(' ')[0]) + transcript_id = entry.header[1:].split(' ')[0] if transcript_id in selected_transcript_ids: - output_fasta_file.write(">%s\n%s\n" % (transcript_id, entry.sequence)) + output_fasta_file.write("%s\n%s\n" % (entry.header, entry.sequence)) |
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| diff -r a07680f3033a -r 6cf9f7f6509c ensembl_longest_cds_per_gene.xml --- a/ensembl_longest_cds_per_gene.xml Tue Mar 07 11:12:55 2017 -0500 +++ b/ensembl_longest_cds_per_gene.xml Wed Mar 15 20:23:13 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ensembl_longest_cds_per_gene" name="Select longest CDS per gene" version="0.0.1"> +<tool id="ensembl_longest_cds_per_gene" name="Select longest CDS per gene" version="0.0.2"> <description>from Ensembl CDS FASTA</description> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/ensembl_longest_cds_per_gene.py' -f '$input' -o '$output' @@ -22,6 +22,6 @@ >ENSMUST00000177965.1 cds chromosome:GRCm38:12:113456720:113456736:-1 gene:ENSMUSG00000094057.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd2-7 description:immunoglobulin heavy diversity 2-7 [Source:MGI Symbol;Acc:MGI:4439866] -Among the CDS sequences having the same gene identifier (ENSMUSG00000094057 in the example above), the tool will select the one with the longest sequence. The header of the sequences in the output dataset will contain only the transcript id without version (ENSMUST00000177965 in the example above). +Among the CDS sequences having the same gene identifier (ENSMUSG00000094057 in the example above), the tool will select the one with the longest sequence. ]]></help> </tool> |
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| diff -r a07680f3033a -r 6cf9f7f6509c test-data/Mus_musculus.GRCm38.cds.longest.fa --- a/test-data/Mus_musculus.GRCm38.cds.longest.fa Tue Mar 07 11:12:55 2017 -0500 +++ b/test-data/Mus_musculus.GRCm38.cds.longest.fa Wed Mar 15 20:23:13 2017 -0400 |
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| b'@@ -1,134 +1,134 @@\n->ENSMUST00000196221\n+>ENSMUST00000196221.1 cds chromosome:GRCm38:14:54113468:54113476:1 gene:ENSMUSG00000096749.2 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene gene_symbol:Trdd1 description:T cell receptor delta diversity 1 [Source:MGI Symbol;Acc:MGI:4439547]\n ATGGCATAT\n->ENSMUST00000177564\n+>ENSMUST00000177564.1 cds chromosome:GRCm38:14:54122226:54122241:1 gene:ENSMUSG00000096176.1 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene gene_symbol:Trdd2 description:T cell receptor delta diversity 2 [Source:MGI Symbol;Acc:MGI:4439546]\n ATCGGAGGGATACGAG\n->ENSMUST00000178537\n+>ENSMUST00000178537.1 cds chromosome:GRCm38:6:41533201:41533212:1 gene:ENSMUSG00000095668.1 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene gene_symbol:Trbd1 description:T cell receptor beta, D region 1 [Source:MGI Symbol;Acc:MGI:4439571]\n GGGACAGGGGGC\n->ENSMUST00000178862\n+>ENSMUST00000178862.1 cds chromosome:GRCm38:6:41542163:41542176:1 gene:ENSMUSG00000094569.1 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene gene_symbol:Trbd2 description:T cell receptor beta, D region 2 [Source:MGI Symbol;Acc:MGI:4439727]\n GGGACTGGGGGGGC\n->ENSMUST00000179520\n+>ENSMUST00000179520.1 cds chromosome:GRCm38:12:113430528:113430538:-1 gene:ENSMUSG00000094028.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd4-1 description:immunoglobulin heavy diversity 4-1 [Source:MGI Symbol;Acc:MGI:4439801]\n CTAACTGGGAC\n->ENSMUST00000179883\n+>ENSMUST00000179883.1 cds chromosome:GRCm38:12:113448214:113448229:-1 gene:ENSMUSG00000094552.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd3-2 description:immunoglobulin heavy diversity 3-2 [Source:MGI Symbol;Acc:MGI:4439707]\n AGACAGCTCAGGCTAC\n->ENSMUST00000195858\n+>ENSMUST00000195858.1 cds chromosome:GRCm38:12:113449588:113449597:-1 gene:ENSMUSG00000096420.2 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd5-6 description:immunoglobulin heavy diversity 5-6 [Source:MGI Symbol;Acc:MGI:4937234]\n GAATACCTAC\n->ENSMUST00000180001\n+>ENSMUST00000180001.1 cds chromosome:GRCm38:12:113450851:113450867:-1 gene:ENSMUSG00000095656.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd2-8 description:immunoglobulin heavy diversity 2-8 [Source:MGI Symbol;Acc:MGI:4439706]\n TCTACTATGGTAACTAC\n->ENSMUST00000178815\n+>ENSMUST00000178815.1 cds chromosome:GRCm38:12:113454942:113454951:-1 gene:ENSMUSG00000094957.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd5-5 description:immunoglobulin heavy diversity 5-5 [Source:MGI Symbol;Acc:MGI:4937334]\n GACTACCTAC\n->ENSMUST00000177965\n+>ENSMUST00000177965.1 cds chromosome:GRCm38:12:113456720:113456736:-1 gene:ENSMUSG00000094057.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd2-7 description:immunoglobulin heavy diversity 2-7 [Source:MGI Symbol;Acc:MGI:4439866]\n TCTACTATGGTTACGAC\n->ENSMUST00000178909\n+>ENSMUST00000178909.1 cds chromosome:GRCm38:12:113459864:113459892:-1 gene:ENSMUSG00000094268.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd5-8 description:immunoglobulin heavy diversity 5-8 [Source:MGI Symbol;Acc:MGI:4937171]\n AGACAGCTAGCCTCTGCAGTGCCACAACC\n->ENSMUST00000177646\n+>ENSMUST00000177646.1 cds chromosome:GRCm38:12:113460101:113460110:-1 gene:ENSMUSG00000096884.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd5-4 description:immunoglobulin heavy diversity 5-4 [Source:MGI Symbol;Acc:MGI:4937058]\n GAATACCTAC\n->ENSMUST00000178230\n+>ENSMUST00000178230.1 cds chromosome:GRCm38:12:113461369:113461385:-1 gene:ENSMUSG00000096250.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd2-6 description:immunoglobulin heavy diversity 2-6 [Source:MGI Symbol;Acc:MGI:4439865]\n CCTACTATAGTAACTAC\n->ENSMUST00000178483\n+>ENSMUST00000178483.1 cds chromosome:GRCm38:12:113464524:113464552:-1 gene:ENSMUSG00000095592.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd5-7 description:immunoglobulin heavy diversity 5-7 [Source'..b'ion:T cell receptor alpha variable 13-1 [Source:MGI Symbol;Acc:MGI:4439904]\n ATGAAGAGGCTGCTGAGCTCTCTGCTGGGGCTTCTGTGCACCCAGGTTTGCTGGGTGAAA\n GGACAGCAAGTGCAGCAGAGCCCCGCGTCCTTGGTTCTGCAGGAGGGGGAGAACGCAGAG\n CTGCAGTGTAACTTTTCCACATCTTTGAACAGTATGCAGTGGTTTTACCAACGTCCTGGG\n GGAAGTCTCGTCAGCCTGTTCTACAATCCTTCTGGGACAAAGCATAGTGGGAGACTGACA\n TCCACTACAGTCATCAAAGAACGTCGCAGCTCTTTGCACATTTCCTCCTCCCAGACAACA\n GACTCAGGCACTTATCTCTGTGCTTTGGAAC\n->ENSMUST00000198297\n+>ENSMUST00000198297.1 cds chromosome:GRCm38:14:53554022:53554558:1 gene:ENSMUSG00000076840.4 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene gene_symbol:Trav14-1 description:T cell receptor alpha variable 14-1 [Source:MGI Symbol;Acc:MGI:3646773]\n ATGGACAAGATTCTGACAGCATCATTTTTACTCCTAGGCCTTCACCTAGCTGGGGTGAAT\n GGCCAGCAGAAGGAGAAACATGACCAGCAGCAGGTGAGACAAAGTCCCCAATCTCTGACA\n GTCTGGGAAGGAGGAACCACAGTTCTGACCTGCAGTTATGAGGACAGCACTTTTAACTAC\n@@ -136,35 +136,35 @@\n GTGTCCGATAAAAAGGAAGATGGACGATTCACAACCTTCTTCAATAAAAGGGAGAAAAAG\n CTCTCCTTGCACATCATAGACTCTCAGCCTGGAGACTCAGCCACCTACTTCTGTGCAGCA\n AGTG\n->ENSMUST00000200101\n+>ENSMUST00000200101.1 cds chromosome:GRCm38:14:53559632:53560247:1 gene:ENSMUSG00000094016.2 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene gene_symbol:Trav15-1-dv6-1 description:T cell receptor alpha variable 15-1-DV6-1 [Source:MGI Symbol;Acc:MGI:4439369]\n ATGCCTCCTCACAGCCTGCTCTGTGTGCTGGTGGCCTTGGCTTTCTCTGGATCTAATGTG\n GCCCAGAAAGTGATTCAGGTCTGGTCAACAACAAGCAGGCAGGAGGGCGAAAAACTCACA\n CTGGACTGTTCATATAAGACAAGTCAGGTCTTATACCATCTTTTCTGGTACAAGCACCTT\n CTTAGTGGAGAGATGGTTTTGCTTATTCGACAAATGCCTTCTACTATTGCAATAGAGAGG\n AGCGGCCGCTATTCTGTAGTCTTCCAGAAATCACGCAAATCCATCAGCCTTGTCATTTCA\n ACCTTACAACCAGACGATTCGGGAAAGTATTTCTGTGCTCTCTGGGAGCTGG\n->ENSMUST00000103654\n+>ENSMUST00000103654.2 cds chromosome:GRCm38:14:53590857:53591514:1 gene:ENSMUSG00000094966.2 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene gene_symbol:Trav9-2 description:T cell receptor alpha variable 9-2 [Source:MGI Symbol;Acc:MGI:4439903]\n ATGCTCCTGGCGCTCCTCCCAGTGCTGGGGATACACTTTGTCCTGAGAGATGCCCAAGCT\n CAGTCAGTGACGCAGCCCGATGCTCGCGTCACTGTCTCTGAAGGAGCCTCTCTGCAGCTG\n AGATGCAAGTATTCCTACTCTGGGACACCTTATCTGTTCTGGTATGTCCAGTACCCGCGG\n CAGGGGCTGCAGCTGCTCCTCAAGTACTATTCAGGAGACCCAGTGGTTCAAGGAGTGAAT\n GGCTTCGAGGCTGAGTTCAGCAAGAGTAACTCTTCCTTCCACCTGCGGAAAGCCTCTGTG\n CACTGGAGCGACTCTGCTGTGTACTTCTGTGTTTTGAGCG\n->ENSMUST00000103655\n+>ENSMUST00000103655.2 cds chromosome:GRCm38:14:53598828:53599410:1 gene:ENSMUSG00000093966.2 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene gene_symbol:Trav4-3 description:T cell receptor alpha variable 4-3 [Source:MGI Symbol;Acc:MGI:4440478]\n ATGCAGAGGAACCTGGGAGCTGTGCTGGGGATTCTGTGGGTGCAGATTTGCTGGGTGAGC\n GGAGATAAGGTGAAACAAAGTCCCTCAGCGCTGAGTCTCCAAGAAGGAACCAATTCTGCT\n CTGAGATGCAATTTTTCTATCGCCGCGACAACTGTGCAGTGGTTCCTACAGAATCCCAGG\n GGCAGCCTCATCAATCTTTTTTACCTGGTTCCAGGAACAAAGGAGAATGGGAGGTTAAAG\n TCAGCATTCGATTCTAAGGAGAGCTACAGCACCCTGCACATCAGGGATGCCCAGCTGGAG\n GACTCAGGCACTTACTTCTGTGCTGCTGAGG\n->ENSMUST00000180972\n+>ENSMUST00000180972.2 cds chromosome:GRCm38:14:53616315:53616914:1 gene:ENSMUSG00000096656.6 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene gene_symbol:Trav12-2 description:T cell receptor alpha variable 12-2 [Source:MGI Symbol;Acc:MGI:5293447]\n ATGAACATGCGTCCTGACACCTGCTCAGTTCTTGTGCTCCTCTTAATGCTCAGAAGGAAC\n AATGGAGACTCTGTGACCCAGACAGAAGGCCTGGTCACTCTCACCGAGGGGTTGCCTGTG\n ATGCTGAACTGCACCTATCAGAGTACTTACTCACCTTTCCTTTTCTGGTATGTGCAACAT\n CTCAACGAAGCCCCTAAGCTACTTTTGAAGAGCTTCACAGACAACAAGAGGCCCGAGCAC\n CAAGGGTTCCACGCCACTCTCCATAAGAGCAGCAGCTCCTTCCATCTGCAGAAGTCCTCA\n GCGCAGCTGTCAGACTCTGCCCTGTACTACTGTGCTTTGAGTGA\n->ENSMUST00000103657\n+>ENSMUST00000103657.5 cds chromosome:GRCm38:14:53621657:53622245:1 gene:ENSMUSG00000095958.3 gene_biotype:TR_V_gene transcript_biotype:TR_V_gene gene_symbol:Trav12-3 description:T cell receptor alpha variable 12-3 [Source:MGI Symbol;Acc:MGI:3648633]\n ATGCGTCCTGGCACCTGCTCAGTTCTTGTGCTCCTCCTAATGCTCAGGAGGAGCAATGGA\n GATGGAGACTCAGTGACCCAGAAGGAAGGCCTGGTCACTCTCACCGAGGGGTTGCCTGTG\n ATGCTGAACTGCACCTATCAGACTATTTACTCAAATGCTTTCCTTTTCTGGTATGTGCAC\n' |