# HG changeset patch # User gregory-minevich # Date 1332255484 14400 # Node ID 80d72a1dbd1393b888bd508b48472b89d2c5898d Uploaded diff -r 000000000000 -r 80d72a1dbd13 ._bcftools_view.py Binary file ._bcftools_view.py has changed diff -r 000000000000 -r 80d72a1dbd13 ._bcftools_view.xml Binary file ._bcftools_view.xml has changed diff -r 000000000000 -r 80d72a1dbd13 bcftools_view.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_view.py Tue Mar 20 10:58:04 2012 -0400 @@ -0,0 +1,53 @@ +#!/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 000000000000 -r 80d72a1dbd13 bcftools_view.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_view.xml Tue Mar 20 10:58:04 2012 -0400 @@ -0,0 +1,151 @@ + + 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 + + + +