# HG changeset patch # User gregory-minevich # Date 1349727109 14400 # Node ID 5900b31a9ae91e151e9a5859585f4dad26021f8c # Parent 69e3ff62728f12f0744e6d79ea19659ed1f2bd22 Deleted selected files diff -r 69e3ff62728f -r 5900b31a9ae9 bcftools_view.py --- 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__() diff -r 69e3ff62728f -r 5900b31a9ae9 bcftools_view.xml --- 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 @@ - - Converts BCF format to VCF format - - samtools - - - 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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -**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.) - - -