Mercurial > repos > drosofff > msp_sr_bowtie_parser
changeset 2:70193ce0540e draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | mvdbeek |
|---|---|
| date | Thu, 11 Jun 2015 10:15:20 -0400 |
| parents | f5388910d083 |
| children | 3fcc752a7101 |
| files | sRbowtieParser.py sRbowtieParser.xml tool_dependencies.xml |
| diffstat | 3 files changed, 29 insertions(+), 21 deletions(-) [+] |
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--- a/sRbowtieParser.py Sun Mar 29 11:27:33 2015 -0400 +++ b/sRbowtieParser.py Thu Jun 11 10:15:20 2015 -0400 @@ -1,11 +1,15 @@ #!/usr/bin/python # python parser module to analyse sRbowtie alignments -# version 1.0.0 - argparse implementation +# version 1.0.2 - argparse implementation # Usage sRbowtieParser.py <1:index source> <2:extraction directive> <3:outputL> <4:polarity> <5:6:7 filePath:FileExt:FileLabel> <.. ad lib> import sys, argparse from smRtools import * +def masterListGenerator(data_source): + for filePath, FileExt, FileLabel in data_source: + yield HandleSmRNAwindows (filePath, FileExt, IndexSource, genomeRefFormat) + def Parser(): the_parser = argparse.ArgumentParser() the_parser.add_argument('--IndexSource', action="store", type=str, help="Path to the index source") @@ -24,22 +28,30 @@ genomeRefFormat = args.ExtractDirective Output = args.output Polarity = args.polarity -MasterListOfGenomes = {} +header = ["gene"] + + +FileLabelList=[label for label in args.alignmentLabel] +header.extend(FileLabelList) +assert (len(FileLabelList)==len(set(FileLabelList))),"You have supplied a non-unique label. Please make sure that your input files have unique names" -for filePath, FileExt, FileLabel in zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel): - MasterListOfGenomes[FileLabel] = HandleSmRNAwindows (filePath, FileExt, IndexSource, genomeRefFormat) +data_source=zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel) +master_generator=masterListGenerator(data_source) -header = ["gene"] -for filePath, FileExt, FileLabel in zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel): - header.append(FileLabel) +for i,window in enumerate(master_generator): + window=window + if i==0: + gene_count_dict={gene:[str(item.readcount(polarity=Polarity))] for gene,item in window.instanceDict.items()} + else: + [gene_count_dict[gene].append(str(item.readcount(polarity=Polarity))) for gene,item in window.instanceDict.items()] + F = open (args.output, "w") # print >>F, args print >> F, "\t".join(header) -for item in sorted (MasterListOfGenomes[header[1]].instanceDict.keys() ): + +for item in sorted(gene_count_dict.keys()): line=[item] - for sample in header[1:]: - count = str (MasterListOfGenomes[sample].instanceDict[item].readcount(polarity=Polarity)) - line.append(count) + line.extend(gene_count_dict[item]) print >> F, "\t".join(line ) F.close()
--- a/sRbowtieParser.xml Sun Mar 29 11:27:33 2015 -0400 +++ b/sRbowtieParser.xml Thu Jun 11 10:15:20 2015 -0400 @@ -1,11 +1,10 @@ -<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.1"> +<tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.2"> <description></description> <requirements> <requirement type="package" version="0.12.7">bowtie</requirement> <requirement type="package" version="0.1.18">samtools</requirement> <requirement type="package" version="0.7.7">pysam</requirement> - <requirement type="package" version="1.9">numpy</requirement> - <requirement type="package" version="0.14">scipy</requirement> + <requirement type="package" version="0.14">python_2_7_scipy</requirement> </requirements> <command interpreter="python"> sRbowtieParser.py
--- a/tool_dependencies.xml Sun Mar 29 11:27:33 2015 -0400 +++ b/tool_dependencies.xml Thu Jun 11 10:15:20 2015 -0400 @@ -3,16 +3,13 @@ <package name="bowtie" version="0.12.7"> <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="samtools" version="0.1.18"> - <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="samtools" version="1.2"> + <repository changeset_revision="77e0e0891773" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="pysam" version="0.7.7"> <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="numpy" version="1.9"> - <repository changeset_revision="266529386609" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="scipy" version="0.14"> - <repository changeset_revision="2e3809844979" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="python_2_7_scipy" version="0.14"> + <repository changeset_revision="145ba5a36683" name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>