Mercurial > repos > plus91-technologies-pvt-ltd > softsearch

comparison 2.4/src/Extract_nSC.pl @ 13:e3609c8714fb draft

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author plus91-technologies-pvt-ltd
date Fri, 30 May 2014 03:37:55 -0400
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12:980fce54e60a 13:e3609c8714fb
1 #!/usr/bin/perl -w
2
3 use Getopt::Long;
4
5 #Initialize values
6 my (@queries,@HEADER,$samples,@HEADER_OUT,$end,$samp);
7 GetOptions ("query|q=s" => \$queries);
8 if(!$queries){die "Usage: FORMAT_extract.pl <VCF> -query nSC
9 \n\n";}
10
11
12 open (VCF,"$ARGV[0]") or die "Usage: <VCF>";
13
14 while (<VCF>) {
15 if($_=~/^##/){print;next}
16 chomp;
17 @line=split(/\t/,$_);
18 if($line[0]=~/^#CH/){
19 print join ("\t",@line,$queries)."\n";
20 next}
21 @FORMAT=split(/:/,$line[8]);
22 @SAMPLE=split(/:/,$line[9]);
23 for($i=0;$i<@FORMAT;$i++){
24 if($FORMAT[$i] =~/^$queries$/){print join ("\t",@line,$SAMPLE[$i])."\n";next}
25 }
26 }
27 close VCF;