Mercurial > repos > nilesh > somatic_sniper
view somatic_sniper_wrapper.pl @ 11:7c44a77693f8 draft
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author | nilesh |
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date | Fri, 28 Jun 2013 16:53:39 -0400 |
parents | 2e66a79fe57f |
children |
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use strict; use warnings; use File::Basename; use Cwd; use File::Path qw(make_path remove_tree); die qq( Bad numbr of inputs ) if(!@ARGV); my $options =""; my $normal=""; my $tumor=""; my $output=""; foreach my $input (@ARGV) { my @tmp = split "::", $input; if($tmp[0] eq "NORMAL") { $normal = $tmp[1]; } elsif($tmp[0] eq "TUMOR") { $tumor = $tmp[1]; } elsif($tmp[0] eq "OUTPUT") { $output = $tmp[1]; } elsif($tmp[0] eq "OPTION") { $options = "$options ${tmp[1]}"; } else { die("Unknown Input: $input\n"); } } my $working_dir = cwd(); system ("ln -s $normal $working_dir/normal.bam"); system ("samtools index $working_dir/normal.bam"); system ("ln -s $tumor $working_dir/tumor.bam"); system ("samtools index $working_dir/tumor.bam"); system ("bam-somaticsniper $options $working_dir/tumor.bam $working_dir/normal.bam $output");