Mercurial > repos > geert-vandeweyer > bamtools_wrappers

comparison SplitOnRg.pl @ 0:afa51021226c draft

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author geert-vandeweyer
date Tue, 18 Feb 2014 04:18:08 -0500
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-1:000000000000 0:afa51021226c
1 #!/usr/bin/perl
2
3 use Getopt::Std;
4 getopts('i:o:O:k:p:', \%opts) ;
5
6
7 # split
8 $prefix = "primary_$opts{'O'}"."_";
9 $command = "cd $opts{'p'} && bamtools split -in $opts{'i'} -tag RG -tagPrefix '$prefix' -stub $opts{'p'}/data" ;
10 #print $command ."\n";
11 system($command);
12 chdir($opts{'p'});
13 # rename to correct format.
14 my @ls = `ls data.primary_$opts{'O'}_RG_*`;
15 open OUT, ">$opts{'o'}";
16 $idx = 0;
17 foreach(@ls) {
18 chomp();
19 my $from = $_;
20 $from =~ m/(.*_RG_)(.*)(\.bam)/;
21 my $rg = $2;
22 # remove data_
23 my $to = substr($from,5,-4);
24 $to .= "_visible_bam_$opts{'k'}";
25 $to =~ s/RG_//;
26 $to =~ m/primary_(\d+)_(.*)_visible.*/;
27 $rgreplace = $2;
28 $rgreplace =~ s/\.|-|_//g;
29 $to =~ s/(primary_\d+_)(.*)(_visible.*)/$1$rgreplace$3/;
30 system("mv $from $to");
31 $idx++;
32 print OUT "File $idx : $to : ReadGroup: $rg\n";
33 }
34 close OUT;
35 exit;
36
37