Mercurial > repos > completegenomics > cg_cgatools_linux
view cgatools/tools/cgatools_1.5/varfilter_wrapper.pl @ 0:182426b32995 draft default tip
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author | completegenomics |
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date | Mon, 18 Jun 2012 20:15:00 -0400 |
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#!/usr/bin/perl use strict; use Getopt::Long; use vars qw($opt_reference $opt_input $opt_output @opt_zygosity @opt_vartype @opt_varscorevaf @opt_varscoreeaf @opt_varquality); $| = 1; # set autoflush to screen # This is a wrapper for the cgatools varfilter function to run cgatools varfilter in Galaxy. # The wrapper generates the filter(s) in the correct format to be used with the input file. # written 6-1-2012 by bcrain@completegenomics.com #print join("\n", @ARGV), "\n"; &GetOptions("reference=s", "input=s", "output=s", "zygosity=s@", "vartype=s@", "varscorevaf=s@", "varscoreeaf=s@", "varquality=s@"); my $append = ''; for (my $i = 0; $i <= $#opt_zygosity; $i ++) { my $filter = ''; unless ($opt_zygosity[$i] eq 'NA') {$filter = $opt_zygosity[$i];} unless ($opt_vartype[$i] eq 'NA') { $filter ne '' and $filter .= ':'; $filter .= 'varType=' . $opt_vartype[$i]; } unless ($opt_varscorevaf[$i] eq 'x') { $filter ne '' and $filter .= ':'; $opt_varscorevaf[$i] =~ s/^x//; $filter .= 'varScoreVAF<' . $opt_varscorevaf[$i]; } unless ($opt_varscoreeaf[$i] eq 'x') { $filter ne '' and $filter .= ':'; $opt_varscoreeaf[$i] =~ s/^x//; $filter .= 'varScoreEAF<' . $opt_varscoreeaf[$i]; } unless ($opt_varquality[$i] eq 'NA') { $filter ne '' and $filter .= ':'; $filter .= 'varQuality!=' . $opt_varquality[$i]; } if ($filter ne '') { if ($append eq '') {$append = '#' . $filter;} else {$append .= ',' . $filter;} } } print "cgatools varfilter --beta --reference $opt_reference --output $opt_output --input '${opt_input}${append}'\n"; `cgatools varfilter --beta --reference $opt_reference --output $opt_output --input '${opt_input}${append}'`;