Mercurial > repos > fcaramia > jointsnvmix
view joint_snv_mix.pl @ 1:7fb20f2d156c draft
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author | fcaramia |
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date | Thu, 20 Jun 2013 00:53:13 -0400 |
parents | a1034918ab9b |
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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 $bam_normal; my $bam_tumor; my $player_options = ""; my $output; my $action; my $ref_genome; foreach my $input (@ARGV) { my @tmp = split "::", $input; if($tmp[0] eq "BAMNORMAL") { $bam_normal = $tmp[1]; } elsif($tmp[0] eq "BAMTUMOR") { $bam_tumor = $tmp[1]; } elsif($tmp[0] eq "OPTION") { $player_options = "$player_options ${tmp[1]}"; } elsif($tmp[0] eq "REFGENOME") { $ref_genome = $tmp[1]; } elsif($tmp[0] eq "ACTION") { $action = $tmp[1]; } elsif($tmp[0] eq "OUTPUT") { $output = $tmp[1]; } else { die("Unknown Input: $input\n"); } } #Create Symbolic links and indexes my $working_dir = cwd(); system ("ln -s $bam_normal $working_dir/normal.bam"); system ("samtools index $working_dir/normal.bam"); system ("ln -s $bam_tumor $working_dir/tumor.bam"); system ("samtools index $working_dir/tumor.bam"); #run jsm if($action eq "classify") { system ("jsm.py $action $player_options $ref_genome $working_dir/normal.bam $working_dir/tumor.bam"); } else { system ("jsm.py $action $player_options $ref_genome $working_dir/normal.bam $working_dir/tumor.bam $output"); }