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

comparison 2.4/src/Merge_Soft.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 -s
2 #Merge Softsearch results by chrom
3 if(!$ARGV[0]){die "Usage: <Sample.1.vcf>\n";}
4 my ($sample,$cmd);
5
6 #Get basename
7 $sample="$ARGV[0]";
8 $sample=~s/.[0-9(+)].out.vcf//;
9 $sample=~s/.[0-9(+)].pe.vcf//;
10
11 my $outfile=$sample;
12 $outfile.="out.vcf";
13 if( -e $outfile ){unlink($outfile)}
14 $cmd="ls $sample\*vcf";
15 my @samples=`$cmd`;
16 print "there are " .scalar(@samples)." samples\n";
17
18 open (OUT,">$outfile");
19 my $i=1;
20 my $tmp=@samples[$i];
21 open(TMP,"$tmp");
22 while (<TMP>){
23 print OUT if ($_=~/^#/);
24 }
25
26 open (OUT,">>$outfile");
27 my $chr;
28 for (my $i=0;$i<@samples;$i++){
29 my $tmp=@samples[$i];
30 open(TMP,"$tmp");
31 while (<TMP>){
32 unless (($_=~/^chrGL/)||($_=~/^#/)){print OUT $_;}
33 }
34 print "Done with $tmp";
35 unlink($tmp);
36 system("rm $tmp");
37 close TMP;
38 }
39 close OUT;