| Previous changeset 1:922d69bd5258 (2013-01-29) Next changeset 3:6a14074bc810 (2013-07-29) |
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Commit message:
Uploaded v0.0.3, bundle Ssuis.fasta test file X record Python script version |
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modified:
tools/filters/get_orfs_or_cdss.py tools/filters/get_orfs_or_cdss.txt tools/filters/get_orfs_or_cdss.xml |
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added:
test-data/Ssuis.fasta |
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| diff -r 922d69bd5258 -r 324775a016ce test-data/Ssuis.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Ssuis.fasta Tue Apr 23 11:48:43 2013 -0400 |
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| b'@@ -0,0 +1,33460 @@\n+>Streptococcus_suis\n+ATGAACCAAGAACAACTTTTTTGGCAACGATTTATTGAATTGGCAAAGGTAAATTTTAAG\n+CCATCTATTTATGATTTTTATGTCGCTGATGCAAAATTACTCGGAATCAACCAGCAAGTT\n+GCCAATATTTTCTTAAATCGTCCATTTAAAAAAGATTTCTGGGAAAAAAACTTCGAAGAG\n+TTAATGATTGCCGCTAGTTTTGAAAGCTACGGAGAGCCTCTTACCATCCAATATCAATTT\n+ACAGAGGATGAACAGGAGATTAGGAATACTACAAACACAAGAAGTTCAATAGTTCACCAG\n+GTACAGACACTTGAGCCGGCTACTCCTCAAGAAACTTTTAAACCGGTTCATTCTGATATA\n+AAATCCCAGTACACCTTTGCTAATTTTGTACAAGGAGACAATAATCACTGGGCAAAGGCT\n+GCAGCTTTAGCTGTATCTGATAACCTAGGTGAGCTCTACAATCCATTATTCATTTTTGGT\n+GGTCCTGGTCTTGGAAAAACTCATATTTTAAATGCGATTGGAAATAAGGTTCTAGCCGAT\n+AATCCCCAGGCAAGGATAAAATATGTCTCATCGGAAACATTCATCAATGAATTTTTAGAA\n+CACCTCCGTCTCAATGATATGGAAAGTTTCAAAAAAACCTATCGCAATCTGGACTTACTT\n+CTAATTGATGACATTCAGTCTCTCCGTAATAAAGCAACAACACAGGAAGAATTTTTCCAT\n+ACTTTTAATGCGCTTCATGAAAAAAATAAGCAGATTGTACTCACAAGCGACCGTAATCCC\n+GATCACTTAGACAATTTGGAAGAAAGACTAGTAACACGTTTCAAATGGGGGTTAACCAGT\n+GAAATCACTCCACCTGATTTTGAAACACGTATCGCAATTTTACGTAACAAGTGCGAGAAC\n+CTGCCTTACAACTTTACAAATGAGACGCTATCCTATCTAGCTGGGCAATTTGATTCGAAC\n+GTACGTGACCTTGAAGGTGCCTTAAAAGATATCCATTTGATAGCCACTATGCGTCAACTG\n+TCTGAGATAAGTGTCGAGGTTGCTGCTGAGGCTATTCGATCAAGAAAACAAACAAATCCA\n+CAAAACATGGTTATTCCTATTGAGAAAATCCAAACCGAAGTGGGAAATTTCTACGGTGTC\n+AGCTTGAAAGAATTAAAAGGTTCTAAGCGTGTTCAACATATCGTTCACGCGCGACAAGTT\n+GCTATGTTTTTAGCACGTGAAATGACAGACAATTCCCTTCCAAAAATTGGGAAAGAATTT\n+GGTAATCGAGACCATACAACCGTTATGCATGCATACAATAAAATAAAAACTCTCCTCTTG\n+GATGATGAGAATTTAGAAATAGAGATTACCAGTATAAAAAATAAACTTCGTTAACCTGTG\n+TATAACTTTTTTAAAAAACTCTGTTTTTTCCACAAGTTGTGAACAAGTTAATTTCCGCAG\n+TTTTATTGGTCTTTCATCACTTTTCCACAGAATACACAGAGACTACTATTACTATTAACC\n+TTATAGATAATAAATAAAGGAGAATCCATGATTCAATTTTCTATTAATAAAAATATATTT\n+CTACAAGCACTTAGTATTACTAAACGGGCAATCAGTACAAAAAATGCTATTCCAATTCTT\n+TCAACAGTAAAAATTACAGTAACTAGTGAAGGAATCACTTTAACTGGTTCAAATGGACAA\n+ATCTCGATAGAACATTTTATTTCTATTCAAGATGAAAATGCAGGGCTTTTGATCAGTTCT\n+CCAGGTTCCATTCTCTTAGAAGCTGGTTTCTTTATTAATGTCGTATCCAGTATGCCGGAT\n+TTGGTCCTTGACTTCAATGAAATTGAACAAAAGCAAATCGTTTTGACAAGTGGTAAGTCT\n+GAAATCACATTAAAGGGAAAAGAAGCAGAACAGTATCCTCGTTTACAGGAAGTTCCAACT\n+TCAAAACCATTGGTGTTAGAAACCAAAGTATTAAAACAAACAATTAATGAAACAGCATTT\n+GCAGCTTCTACACAAGAAAGTCGTCCTATTCTTACGGGTGTTCATTTTGTTTTAACAGAA\n+AATAAAAATCTAAAAACTGTTGCAACAGATTCACACCGTATGAGCCAACGGAAATTGGTC\n+CTTGATACCTCTGGTGATGATTTTAATGTTGTCATTCCAAGTCGTTCTCTCCGTGAATTT\n+ACTGCAGTTTTTACAGATGATATTGAAACAGTAGAAGTCTTCTTTTCAAATAATCAAATC\n+CTTTTTAGAAGCGAGCATATTAGCTTCTATACACGCTTATTAGAAGGTACCTACCCTGAT\n+ACCGACCGCTTAATTCCAACTGAGTTTAAAACAACTGCAATTTTTGATACTGCAAATCTT\n+CGTCACTCGATGGAGCGTGCTCGTCTTCTTTCAAATGCAACCCAAAATGGTACAGTAAAA\n+CTAGAAATTGCTAATAATGTTGTATCGGCTCATGTAAATTCTCCAGAAGTTGGACGTGTG\n+AATGAGGAATTAGATACTGTAGAAGTATCAGGTGAAGATTTAGTAATCAGCTTTAACCCA\n+ACTTACTTGATAGAAGCATTGAAAGCCACAACTAGTGAACAAGTGAAAATTAGCTTTATC\n+TCTTCTGTCCGTCCATTTACATTGATTCCAAATAATGAAGGGGAAGATTTTATTCAATTG\n+GTTACACCAGTTCGTACCAACTAAATAATATTAAGAACGGCTAAACTAGCCGTTTTTATG\n+TTATACTAAAAAATAGCACCTAGCTTATTTTTATATATTTAGTGATGGGGAATAAATGAC\n+GTTATATATATTAGCTAATCCTAATGCTGGTAGCCATACTGCTGAACATATCATATTCAA\n+AATAAAAGAAAGTTATCCACAGCTTGCAGTTAACATTTTTATGACAGTTGGTCCTGAGGA\n+TGAAAAAAGTCAAATAGAGGCTATTTTAAAGGAGTTTGTCAGTAGTGAAGATCAATTAAT\n+GATTTTAGGCGGAGACGGCACACTATCTAAAGCTTTGCGTTTTTGGCCAGCTAGTCTACC\n+GTTTGCTTATTATCCAACAGGATCTGGAAATGATTTTGCTAAGGCAATGAATATAACATC\n+GCTATATAGAAGTGTAGATGCCATTTTAGAGAGAAAAACAAGTCGGATATATGTTTTAAA\n+CAGTTCATACGGAACGGTTGTAAACAGTATGGATTTTGGCTTTGCAGCTCAAGTTATCAA\n+TGGTTCAACGAATTCAATTTTGAAAAAAATTCTGAACAAGGTAAAACTTGGGAAGTTAAC\n+TTATCTATTCTTTGGTATTAAAACATTATTTTCAAAACAAGCTATAAACTTAGAATTAAC\n+TCTTGATGAAAAATCTTATCAGTTAGATAATCTCTTTTTTATTTCTGTAGCAAATAGTCT\n+TTATTTTGGTGGAGGAATCATGATATGGCCAACAGCAAGTGCTAAAAAGAAGGAAGTAGA\n+TATTGTTTACTTCAAAAATGGAAATTTCTACCAACGTCTACAATCATTGTTAGCCTTATT\n+AACGAAGAGGCATGAATCTTCTCATACGATTCAGCATTTAACAGGGGTAGATGTAGTTTT\n+AAAATCAAAAGAAAAATTATTATTGCAAATAGATGGAGAGACATGCACTGCAAATGAGGT\n+AACGTTAACCTATCAGGAAAGAAGTATGTATCTTTAAGGAGGAAGTATGTACCAATTAGG\n+AACCTTTGTCGAAATGAAAAAGCCCCATGCCTGTGTCATCAAATCGACCGGAAAGAAGGC\n+TAATAAATGGGAGGTTATCCGTCTAGGAGCGGATATTAAAATCCGCTGTACCAACTGTGA\n+CCATGTCGTTATGATGAGCCGGCATGATTTTGAACGAAAAATGAAACAAGT'..b'CTCTACCAACTGAGCTA\n+TGGCGGAAGAAATAGTCCGTACGGGATTCGAACCCGTGTTACCGCCGTGAAAAGGCGGTG\n+TCTTAACCCCTTGACCAACGGACCATTTTTAGAACAATAACTAGTATAATACATGTGACT\n+TTGTTTGTCAATACATTTTTTGATTTTTTATTGTATTGACAGAGTGCTTTGTTTAATGTA\n+AAATAAAATGGTTAAGGTTCCATAGCTCAGCTGGATAGAGCATTCGCCTTCTAAGCGAAC\n+GGTCGCAGGTTCGAATCCTGCTGGAATCATTTAGACCTACCTCGAGTAGGTCTTTTTTCT\n+TGCCATAATTCATAATTAATATATAACACTGGCAAAATCAGACCAATAAGGGCATATTCT\n+TCAAATTGGAAGGATAGGTGAGTAGATATGATGACACCTAGCATAAACCCTATAATGGTC\n+AATAAGATGTTTCTACCTGTTTTTCTAAGTTCTGAATCTTTTTCAATAACTCCTTTAAAC\n+CAGAGATAAGCAGCATTTTTGACATTCCCTGTCATCATCACATTGGCATACGGAGCACCT\n+CGTAACCTTCTAAATGTTTCTACTTGAATAGAGGCTACGAAGGCTAGACTAGCAATTGTA\n+AAAGACGCAGGCATTATAGGTGAGAGAATGATAGTTAGTAAAATAAGAACTAACATCATT\n+ACACTACTACCAAAGTGCCAAGACCATGTTTGTTTTTCAAAATACCTTCTTGCTAAGTAG\n+GTAAAAAATTGTCCGAATACAAAAAATAAAATGGGAATGGAAAAATTAACTACCTGCGCA\n+AAATCACCTTTAGCTAAAAAATAAGCTAGGGAAATAACATTTCCAGATTGTACGCCAGCA\n+AAGCGACCACCCTGAGTCACAAAAGTAAAGGCATTTAAATAACCACTGATAAACGTTAAT\n+GAACAAGCAATTCTCAATCCCTCAAAAACACGATACTCTTTTTGATTCATTTTCACTCCT\n+TGTTTCACGTGAAACTACTTATGATATGGGCTTCCCTGCTGAATCATAAATGCACGATAA\n+ATCTGCTCGATGAGAACTAATTTCATTAGTTGATGGGGAAGTGTCAACTGTCCAAAACTC\n+ATCAACAAATTAGCTCTTTTTTTAATACAAGAATCGAGACCCAAACTACCACCGATGATA\n+AAAGTTATATCTGAATACCCATTTACTGCAATGTCAGATATCCTTTGACTAAATTCTTCC\n+GATGGAAATTGTTTCCCTTCTATCGCTAAGGCAATGACAAAATCTCGCTCTCCAATTTTA\n+GACATAATTCTATCGGCTTCTTTTTTTAATATTTGTTCATTCTCTGCCTGACTGGCTTTA\n+TCTGGTGTTTTTTCATCAGGAAGCTCAATCATATCCAACTTAGTAAATCGTCCCAATCGT\n+TTACTATATTCTGCAATACCTTCTTTGAGGTACTTTTCTTTCAATTTTCCAACGGTAATC\n+AATTTTATTTTCATAAAATAATTGTAACATATCCACAAGCATACGACAGAAAATATTTTT\n+AGAAAATCAGGATATGGCTACAGTTTTTCACATAATTCACAGAGTTATCCACAGGTTGTG\n+GATTGATTTTTGAAAACTTTAAGTTATAATTAAGAAAGAAATAGTACTCTTAAGGAAAAT\n+TAAAGAAATGGAAAGGATTCCTTATATGAAAAAATATTTGAAATTTGCGATTTTATTTGT\n+AATTGGATTTTTTGGGGGTCTTATCGGGGCCTTGTCAGCCTCTTTCTTCCAGCCACAGGT\n+GCAACAAGCAAATTCTGCTATCACTAGTGTCAGCAATGTTCAATATAATAATGAAACTTC\n+CACCACAAAAGCTGTAGAGAAAGTACAAAATGCTGTTGTGTCTGTTATTAATTACCAAAA\n+ATCAGCCAACAATAGTCTTGGTGTTATCTTTGGAAATATTGAATCATCTGACGAACTAGC\n+TGTTGCTGGAGAGGGGTCTGGGGTTATCTATAAAAAATATGGTCAATATGCCTATATTGT\n+GACAAATACGCATGTTATTAATAACGCAGAAAAGATTGATATCCTTTTAGCATCTGGAGA\n+AAAAATTAGCGGTGAACTTGTTGGTTCCGATACATATTCTGATATAGCTGTTATAAAAAT\n+ATCAGCAGATAAAGTCACTGCTGTTGCTGAATTTGCTGATTCCGATACAATTAAAGTTGG\n+AGAAACTGCTATCGCAATTGGTAGTCCTCTAGGTAGCGTCTACGCCAATACAGTTACCCA\n+GGGTATTATTTCTAGCTTAAGTCGGACAGTTACTTCACAATCAAAAGATGGACAAACAAT\n+CTCAACTAACGCTATTCAAACTGATACAGCTATCAACCCTGGAAACTCTGGCGGACCGTT\n+AATCAATACCCAAGGACAAGTGATAGGCATTACCTCTAGCAAAATTACCTCAAGTTCTGC\n+AAATAGCTCAGGCGTGGCTGTAGAAGGGTTGGGATTTGCTATTCCTGCAAATGATGCCGT\n+AGCTATTATCAATCAGCTTGAAAAAACTGGACAAGTTAGCCGACCTGCTCTTGGAGTTCA\n+TATGGTTAACTTGACGACCTTGTCAACTAGTCAATTAGAAAAAGCTGGATTATCAAATAC\n+GGAATTAACATCCGGTGTAGTAATTGTCTCTACACAAAGTGGGCTACCTGCAGATGGAAA\n+ATTAGAAACTTTTGATGTTATTACTGAGATTGACGGAGAAGCTATTCAAAATAAGAGTGA\n+CCTCCAGAGCGCTCTCTACAAACATCAAATTGGAGATACAATCACTGTAACTTATTACCG\n+CAATAATCAGAAACAAACTGTTGACATTAAGTTGACACATTCTACAGAAGAACTTAGCGA\n+ATAATTGACAAATGAGACTTTACACAATTGTAAAGTCTCATTTTTTTTGCTAGAATAAGG\n+ATATATGGAAGAATTACGTACACTAAATATTTCAGAAATCCATCCCAATCCCTATCAGCC\n+AAGAATTCATTTTGATGAAAAGGAGCTACTTGAGCTCGCTCAATCTATTAAGGAAAATGG\n+CTTAATTCAACCGATTATTGTAAGAAAATCTTCTATTATCGGATACGAATTATTAGCTGG\n+AGAAAGAAGGTTGCGAGCCAGTCAATTAGCTGGACTGACTACAATACCAGCAGTGGTAAA\n+AGAACTGACTGATGATGATTTACTCTATCAGGCTATCATAGAGAATCTGCAGCGTTCTAA\n+CTTAAATCCGATAGAAGAAGCAGCCTCTTATCAAAAATTGATTAGTAGAGGGTTAACACA\n+TGATGAAGTTGCTCAAATCATGGGAAAATCAAGACCATATATCAGTAATTTATTGCGCCT\n+ACTAAATCTATCATCTCAGACTAAACAAGCTGTAGAAGAAGGAAAAATTTCACAAGGGCA\n+CGCGCGACAATTGGTGTCATTTTCAGAAGAAAAGCAAGCCGAATGGGTTCAACTCATTTT\n+ATCAAAGGATTTAAGTGTGCGTACGCTTGAAAAATTAATAGCTGCAAATAAGAAAAAACA\n+CACTAAGCTTAAACAACGCGACCAATTTTTAAAAGAACAGGAAGATTCACTCAGTAAAAC\n+TCTTGGAACAGCTACAAAAATTATCAAGAAGAAAAACGGGAGCGGAGAAATTCGGATTAG\n+CTTTAATGACCTCGATGAATTCGAAAGAATTATCAACAATTTTAAATAGACTTGTTTACA\n+ATTTATTTTTATAAACACTCTTTTCCACACTAAAATCATTACAAAAAGTCAGGACCAGCA\n+AGGGTTCTGACTTTTATTCACATCTTGTGGAAAACTTTTCTTAACAGTGTGGATTTTAAA\n+AATTATCTGTGGAAAACTTTTGTTTTTTATGGTACACTATTCTAACGAATATAATGTGAA\n+AGGGGGAAAAT\n' 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| diff -r 922d69bd5258 -r 324775a016ce tools/filters/get_orfs_or_cdss.py --- a/tools/filters/get_orfs_or_cdss.py Tue Jan 29 10:19:01 2013 -0500 +++ b/tools/filters/get_orfs_or_cdss.py Tue Apr 23 11:48:43 2013 -0400 |
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| @@ -21,11 +21,15 @@ See accompanying text file for licence details (MIT/BSD style). -This is version 0.0.2 of the script. +This is version 0.0.3 of the script. """ import sys import re +if "-v" in sys.argv or "--version" in sys.argv: + print "v0.0.3" + sys.exit(0) + def stop_err(msg, err=1): sys.stderr.write(msg.rstrip() + "\n") sys.exit(err) |
| b |
| diff -r 922d69bd5258 -r 324775a016ce tools/filters/get_orfs_or_cdss.txt --- a/tools/filters/get_orfs_or_cdss.txt Tue Jan 29 10:19:01 2013 -0500 +++ b/tools/filters/get_orfs_or_cdss.txt Tue Apr 23 11:48:43 2013 -0400 |
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| @@ -38,6 +38,8 @@ v0.0.1 - Initial version. v0.0.2 - Correct labelling issue on reverse strand. - Use the new <stdio> settings in the XML wrappers to catch errors +v0.0.3 - Include unit tests. + - Record Python script version when run from Galaxy. Developers @@ -46,10 +48,10 @@ This script and related tools are being developed on the following hg branch: http://bitbucket.org/peterjc/galaxy-central/src/tools -For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -tar -czf get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.* test-data/get_orf_input*.fasta +$ tar -czf get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.* test-data/get_orf_input*.fasta test-data/Ssuis.fasta Check this worked: @@ -57,6 +59,7 @@ filter/get_orfs_or_cdss.py filter/get_orfs_or_cdss.txt filter/get_orfs_or_cdss.xml +test-data/get_orf_input.fasta test-data/get_orf_input.Suis_ORF.nuc.fasta test-data/get_orf_input.Suis_ORF.prot.fasta test-data/get_orf_input.t11_nuc_out.fasta @@ -65,6 +68,7 @@ test-data/get_orf_input.t11_prot_out.fasta test-data/get_orf_input.t1_nuc_out.fasta test-data/get_orf_input.t1_prot_out.fasta +test-data/Ssuis.fasta Licence (MIT/BSD style) |
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| diff -r 922d69bd5258 -r 324775a016ce tools/filters/get_orfs_or_cdss.xml --- a/tools/filters/get_orfs_or_cdss.xml Tue Jan 29 10:19:01 2013 -0500 +++ b/tools/filters/get_orfs_or_cdss.xml Tue Apr 23 11:48:43 2013 -0400 |
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| @@ -1,5 +1,6 @@ -<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.2"> +<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.0.3"> <description>e.g. to get peptides from ESTs</description> + <version_command interpreter="python">get_orfs_or_cdss.py --version</version_command> <command interpreter="python"> get_orfs_or_cdss.py $input_file $input_file.ext $table $ftype $ends $mode $min_len $strand $out_nuc_file $out_prot_file </command> |