Mercurial > repos > fcaramia > jointsnvmix
comparison 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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-1:000000000000 | 0:a1034918ab9b |
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1 | |
2 use strict; | |
3 use warnings; | |
4 use File::Basename; | |
5 use Cwd; | |
6 use File::Path qw(make_path remove_tree); | |
7 die qq( | |
8 Bad numbr of inputs | |
9 | |
10 ) if(!@ARGV); | |
11 | |
12 my $bam_normal; | |
13 my $bam_tumor; | |
14 my $player_options = ""; | |
15 my $output; | |
16 my $action; | |
17 my $ref_genome; | |
18 | |
19 foreach my $input (@ARGV) | |
20 { | |
21 my @tmp = split "::", $input; | |
22 if($tmp[0] eq "BAMNORMAL") | |
23 { | |
24 $bam_normal = $tmp[1]; | |
25 } | |
26 elsif($tmp[0] eq "BAMTUMOR") | |
27 { | |
28 $bam_tumor = $tmp[1]; | |
29 } | |
30 elsif($tmp[0] eq "OPTION") | |
31 { | |
32 $player_options = "$player_options ${tmp[1]}"; | |
33 } | |
34 elsif($tmp[0] eq "REFGENOME") | |
35 { | |
36 $ref_genome = $tmp[1]; | |
37 } | |
38 elsif($tmp[0] eq "ACTION") | |
39 { | |
40 $action = $tmp[1]; | |
41 } | |
42 elsif($tmp[0] eq "OUTPUT") | |
43 { | |
44 $output = $tmp[1]; | |
45 } | |
46 | |
47 else | |
48 { | |
49 die("Unknown Input: $input\n"); | |
50 } | |
51 } | |
52 | |
53 | |
54 #Create Symbolic links and indexes | |
55 | |
56 my $working_dir = cwd(); | |
57 | |
58 system ("ln -s $bam_normal $working_dir/normal.bam"); | |
59 system ("samtools index $working_dir/normal.bam"); | |
60 | |
61 system ("ln -s $bam_tumor $working_dir/tumor.bam"); | |
62 system ("samtools index $working_dir/tumor.bam"); | |
63 | |
64 | |
65 #run jsm | |
66 | |
67 if($action eq "classify") | |
68 { | |
69 system ("jsm.py $action $player_options $ref_genome $working_dir/normal.bam $working_dir/tumor.bam"); | |
70 } | |
71 else | |
72 { | |
73 system ("jsm.py $action $player_options $ref_genome $working_dir/normal.bam $working_dir/tumor.bam $output"); | |
74 } | |
75 |