projects/radseq/novogene/pickR1orR2XTUreads.pl

   1 #!/usr/bin/env perl
   2 use strict;
   3 use warnings;
   4
   5 die "Usage: $0 <in sam.gz> <out sam.gz>\n" if @ARGV<2;
   6
   7 my $in=shift;
   8 my $out=shift;
   9
  10 open I, '-|', "/bin/gzip -dc $in" or die "Error opening $in: $!\n";
  11 open O, '|-', "/bin/gzip -9c >$out" or die "Error opening $out: $!\n";
  12 open LOG, '>>', 'pickR1orR2XTUreads.log';
  13
  14 while (<I>) {
  15   if (/^@/) {
  16     print O;
  17     next;
  18   }
  19   my $r1 = $_;
  20   my @r1 = split /\t/, $r1;
  21   my $r2 = <I>;
  22   my @r2 = split /\t/, $r2;
  23   if (($r1[1] & 0x40) and ($r2[1] & 0x80) and ($r1[0] eq $r2[0])) {
  24     print O $r1,$r2 if ((grep /XT:A:U/, @r1) or (grep /XT:A:U/, @r2));
  25   } else {
  26     print LOG "Error!\t$in\t$r1[0]\t$r1[1]\t$r2[0]\t$r2[1]\n";
  27     exit;
  28   }
  29 }
  30
  31 print LOG "Complete!\t$in\t$out\n";
  32
  33 close I;
  34 close O;
  35 close LOG;
  36