Mercurial > repos > fcaramia > jointsnvmix
diff joint_snv_mix.pl @ 0:a1034918ab9b draft
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author | fcaramia |
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date | Thu, 20 Jun 2013 00:03:08 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/joint_snv_mix.pl Thu Jun 20 00:03:08 2013 -0400 @@ -0,0 +1,75 @@ + +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"); +} +