Mercurial > repos > jjohnson > defuse
changeset 34:3099cec648e7
Update tool_dependencies, add help
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 15 Oct 2013 17:02:23 -0500 |
| parents | 3e3ebdecb0e1 |
| children | a004033614d4 |
| files | create_reference_dataset.xml defuse_results_to_vcf.py tool_dependencies.xml |
| diffstat | 3 files changed, 13 insertions(+), 6 deletions(-) [+] |
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--- a/create_reference_dataset.xml Fri Sep 06 08:20:41 2013 -0500 +++ b/create_reference_dataset.xml Tue Oct 15 17:02:23 2013 -0500 @@ -89,7 +89,12 @@ <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/> </when> <when value="user_specified"> - <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name" help="Examples: homo_sapiens, mus_musculus, rattus_norvegicus"/> + <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name"> + <help> + Examples: homo_sapiens, mus_musculus, rattus_norvegicus + ftp://ftp.ensembl.org/pub/release-$ensembl_version/fasta/$ensembl_organism/dna/$ensembl_prefix.$ensembl_genome_version.$ensembl_version.dna.chromosome.$chromosome.fa.gz + </help> + </param> <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/> <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/> <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/>
--- a/defuse_results_to_vcf.py Fri Sep 06 08:20:41 2013 -0500 +++ b/defuse_results_to_vcf.py Tue Oct 15 17:02:23 2013 -0500 @@ -97,6 +97,8 @@ ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> ##INFO=<ID=MATEID,Number=1,Type=String,Description="ID of the BND mate"> +##INFO=<ID=MATELOC,Number=1,Type=String,Description="The chrom:position of the BND mate"> +##INFO=<ID=GENESTRAND,Number=2,Type=String,Description="Strands"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend"> ##INFO=<ID=SPLITCNT,Number=1,Type=Integer,Description="number of split reads supporting the prediction"> ##INFO=<ID=SPANCNT,Number=1,Type=Integer,Description="number of spanning reads supporting the fusion"> @@ -255,8 +257,8 @@ info.append('EVERSION') if inversion: info.append('INVERSION') - info1 = [svtype,'MATEID=%s' % mate_id2] + info - info2 = [svtype,'MATEID=%s' % mate_id1] + info + info1 = [svtype,'MATEID=%s;MATELOC=%s:%d' % (mate_id2,gene_chromosome2,genomic_break_pos2)] + info + info2 = [svtype,'MATEID=%s;MATELOC=%s:%d' % (mate_id1,gene_chromosome1,genomic_break_pos1)] + info qual = int(float(fields[columns.index('probability')]) * 255) if columns.index('probability') else '.' vcf1 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome1,genomic_break_pos1, mate_id1, ref1, alt1, qual, filt, ';'.join(info1) ) vcf2 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome2,genomic_break_pos2, mate_id2, ref2, alt2, qual, filt, ';'.join(info2) ) @@ -265,7 +267,7 @@ write_vcf() except Exception, e: print >> sys.stderr, "failed: %s" % e - exit(1) + sys.exit(1) if __name__ == "__main__" : __main__()
--- a/tool_dependencies.xml Fri Sep 06 08:20:41 2013 -0500 +++ b/tool_dependencies.xml Tue Oct 15 17:02:23 2013 -0500 @@ -1,10 +1,10 @@ <?xml version="1.0"?> <tool_dependency> <package name="defuse" version="0.6.1"> - <repository changeset_revision="370c0672e531" name="package_defuse_0_6_1" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="66cb7175c473" name="package_defuse_0_6_1" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.19"> - <repository changeset_revision="06697b4877f9" name="package_samtools_0_1_19" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="bowtie" version="1.0.0"> <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />