diff joint_snv_mix.pl @ 0:a1034918ab9b draft

Uploaded

--- /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");
+}
+