perl/etc/fqlenpad.pl

   1 #!/usr/bin/env perl
   2 =pod
   3 Author: Hu Xuesong @ BIOPIC <galaxy001@gmail.com>
   4 Version: 1.0.0 @ 20120720
   5 =cut
   6 use strict;
   7 use warnings;
   8 use Galaxy::IO;
   9
  10 die "Usage: $0 <pad to len> <fq.gz> [out midfix]\n" if @ARGV<2;
  11 my $padto=shift;
  12 my $inf=shift;
  13 my $outf=shift;
  14
  15 my $main = $inf;
  16 $main =~ s/\.fq(\.gz)$//;
  17 if ($outf) {
  18         $main .= ".$outf"
  19 }
  20 $main .= ".$padto.fq.gz";
  21 warn "\@$padto. From [$inf] to [$main]\n";
  22
  23 my $infh = openfile($inf);
  24 open OUT,'|-',"gzip -9c > $main" or die "Error opening $main: $!\n";
  25 my ($a,$b,$c,$d);
  26 while (<$infh>) {
  27         $a=$_;
  28         chomp($b=<$infh>);
  29         $c=<$infh>;
  30         chomp($d=<$infh>);
  31         if (length($b) < $padto) {
  32                 my $t = $padto - length($b);
  33                 $b .= 'N' x $t;
  34                 $d .= '#' x $t;
  35         } elsif (length($b) == $padto) {
  36                 ;
  37         } else {die;}
  38         print OUT "$a$b\n$c$d\n";
  39 }
  40
  41 close $infh;
  42 close OUT;