Mercurial > repos > nilesh > somatic_sniper

comparison somatic_sniper_wrapper.pl @ 9:2e66a79fe57f draft

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author nilesh
date Fri, 28 Jun 2013 16:36:15 -0400
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8:5e4aa9a970db 9:2e66a79fe57f
1 use strict;
2 use warnings;
3 use File::Basename;
4 use Cwd;
5 use File::Path qw(make_path remove_tree);
6 die qq(
7 Bad numbr of inputs
8
9 ) if(!@ARGV);
10
11 my $options ="";
12 my $normal="";
13 my $tumor="";
14 my $output="";
15
16
17 foreach my $input (@ARGV)
18 {
19 my @tmp = split "::", $input;
20 if($tmp[0] eq "NORMAL")
21 {
22 $normal = $tmp[1];
23 }
24 elsif($tmp[0] eq "TUMOR")
25 {
26 $tumor = $tmp[1];
27 }
28 elsif($tmp[0] eq "OUTPUT")
29 {
30 $output = $tmp[1];
31 }
32 elsif($tmp[0] eq "OPTION")
33 {
34 $options = "$options ${tmp[1]}";
35 }
36
37 else
38 {
39 die("Unknown Input: $input\n");
40 }
41 }
42
43
44 my $working_dir = cwd();
45
46 system ("ln -s $normal $working_dir/normal.bam");
47 system ("samtools index $working_dir/normal.bam");
48
49 system ("ln -s $tumor $working_dir/tumor.bam");
50 system ("samtools index $working_dir/tumor.bam");
51
52 system ("bam-somaticsniper $options $working_dir/tumor.bam $working_dir/normal.bam $output");
53
54