Mercurial > repos > gregory-minevich > bcftools_view
changeset 6:5900b31a9ae9 draft
Deleted selected files
| author | gregory-minevich |
|---|---|
| date | Mon, 08 Oct 2012 16:11:49 -0400 |
| parents | 69e3ff62728f |
| children | 4892b1ac6739 |
| files | bcftools_view.py bcftools_view.xml |
| diffstat | 2 files changed, 0 insertions(+), 216 deletions(-) [+] |
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--- a/bcftools_view.py Mon Jun 25 16:16:28 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,53 +0,0 @@ -#!/usr/bin/env python - -""" -Wrapper that execute a program and its arguments but reports standard error -messages only if the program exit status was not 0 -Example: ./stderr_wrapper.py myprog arg1 -f arg2 -""" - -import sys, subprocess - -assert sys.version_info[:2] >= ( 2, 4 ) - -def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - -def __main__(): - # Get command-line arguments - args = sys.argv - # Remove name of calling program, i.e. ./stderr_wrapper.py - args.pop(0) - # If there are no arguments left, we're done - if len(args) == 0: - return - - # If one needs to silence stdout - #args.append( ">" ) - #args.append( "/dev/null" ) - - cmdline = " ".join(args) - try: - # Run program - proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE ) - returncode = proc.wait() - # Capture stderr, allowing for case where it's very large - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += proc.stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - # Running Grinder failed: write error message to stderr - if returncode != 0: - raise Exception, stderr - except Exception, e: - # Running Grinder failed: write error message to stderr - stop_err( 'Error:\n' + str( e ) ) - - -if __name__ == "__main__": __main__()
--- a/bcftools_view.xml Mon Jun 25 16:16:28 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,163 +0,0 @@ -<tool id="bcftools_view" name="bcftools view" version="0.0.1"> - <description>Converts BCF format to VCF format</description> - <requirements> - <requirements type="package">samtools</requirements> - </requirements> - <command interpreter="python"> - bcftools_view.py bcftools view - #if str( $A ) == "true": - -A - #end if - #if str( $b ) == "true": - -b - #end if - #if $D.seq_dictionary == "true": - -D "$D.input" - #end if - #if str( $F ) == "true": - -F - #end if - #if str( $G ) == "true": - -G - #end if - #if str( $N ) == "true": - -N - #end if - #if str( $S ) == "true": - -S - #end if - #if str( $u) == "true": - -u - #end if - #if str( $c ) == "true": - -c - #end if - #if str( $e ) == "true": - -e - #end if - #if str( $g ) == "true": - -g - #end if - #if $i.alt_indel_snp_ratio == "true": - -i $i.ratio - #end if - #if $p.variant_filter == "true": - -p $p.float_value - #end if - #if $t.mutation_rate == "true": - -t $t.rate - #end if - #if str( $v ) == "true": - -v - #end if - $input - > $output - </command> - <inputs> - <param name="input" type="data" format="bcf" label="Choose a bcf file to view" /> - <param name="A" type="select" label="Retain all possible alternate alleles at variant sites"> - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <param name="b" type="select" label="Output in the BCF format. The default is VCF."> - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <conditional name="D"> - <param name="seq_dictionary" type="select" label="Sequence dictionary (list of chromosome names) for VCF->BCF conversion."> - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <when value="true"> - <param name="input" type="data" format="tabular" label="Sequence dictionary" /> - </when> - </conditional> - <param name="F" type="select" label="Indicate PL is generated by r921 or before (ordering is different)."> - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <param name="G" type="select" label="Suppress all individual genotype information."> - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <param name="N" type="select" label="Skip sites where the REF field is not A/C/G/T"> - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <param name="S" type="select" label="The input is VCF instead of BCF."> - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <param name="u" type="select" label="Uncompressed BCF output."> - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <param name="c" type="select" label="Call variants using Bayesian inference. Automatically performs max-likelihood inference only"> - <option value="true" selected="true">Yes</option> - <option value="false">No</option> - </param> - <param name="e" type="select" label="Perform max-likelihood inference only, including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT."> - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <param name="g" type="select" label="Call per-sample genotypes at variant sites"> - <option value="true" selected="true">Yes</option> - <option value="false">No</option> - </param> - <conditional name="i"> - <param name="alt_indel_snp_ratio" type="select" label="Use alternate INDEL-to-SNP mutation rate, default 0.15."> - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <when value="true"> - <param name="ratio" type="float" label="Ratio (float)" value="0.15" /> - </when> - </conditional> - <conditional name="p"> - <param name="variant_filter" type="select" > - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <when value="true"> - <param name="float_value" type="float" label="Float" value="0.5" /> - </when> - </conditional> - <conditional name="t"> - <param name="mutation_rate" type="select" label="Specify scaled mutation rate for variant calling, default is 0.001."> - <option value="true">Yes</option> - <option value="false" selected="true">No</option> - </param> - <when value="true"> - <param name="rate" type="float" label="Mutation Rate (float)" value="0.001" /> - </when> - </conditional> - <param name="v" type="select" label="Output variant sites only."> - <option value="true" selected="true">Yes</option> - <option value="false">No</option> - </param> - </inputs> - <outputs> - <data format="tabular" name="output" /> - </outputs> - <help> -**What it does:** - -This tool converts BCF files into VCF files using BCFtools view from the SAMtools set of utilities: - -http://samtools.sourceforge.net/samtools.shtml#4 - ------- - -**Citation:** - -For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ - - -If you use this tool within Galaxy, please cite `Gregory Minevich, Danny Park, Richard J. Poole, Daniel Blankenberg, Anton Nekrutenko, and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (2012 In Preparation)`__ - - .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html - -Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.) - - </help> -</tool>