Mercurial > repos > fcaramia > somatic_sniper
comparison somatic_sniper_wrapper.pl @ 0:e81f5649bd4d draft default tip
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author | fcaramia |
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date | Thu, 20 Jun 2013 00:06:01 -0400 |
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-1:000000000000 | 0:e81f5649bd4d |
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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 |