projects/radseq/rawfq2list.pl

   1 #!/bin/env perl
   2 use strict;
   3 use warnings;
   4 use integer;
   5
   6 die "Usage: $0 <fq list> <outfile>\n" if @ARGV != 2;
   7 my ($in,$out)=@ARGV;
   8
   9 open IN,'<',$in or die "Error opening $in: $!\n";
  10 open OUT,'>',$out or die "Error opening $out: $!\n";
  11
  12 my $i=2;
  13 while (<IN>) {
  14         next if /^$/;
  15         ++$i;
  16         chomp;
  17         my $full = $_;
  18         s/\.(fastq|fq)(\.gz)?$// or die "[$_]";
  19         my $extra = $2;
  20         my @path = split /\//;
  21         my $name = pop @path;
  22 #warn "$_\n[$name][@path]\n";
  23         my $isRADSEQ = 'N';
  24         $isRADSEQ = 'Y' if $name =~ /_NoIndex_/;
  25         my $id = (split /[_-]/,$name)[2];
  26         $name =~ /(_R|\.)([12])(_|.)([A-Za-z0-9])*?$/ or die "[$name]";
  27 #warn "$2\n";
  28         my $tmpstr = join('_',$id,($i-$2)/2).".$2";
  29         #$full = `readlink -nf $full`;
  30         print OUT join("\t",$tmpstr,$isRADSEQ,$full),"\n";
  31         if ($isRADSEQ eq 'Y') {
  32                 symlink $full,"work/radseq/$tmpstr.fq$extra";
  33         } else {
  34                 symlink $full,"work/parents/$tmpstr.fq$extra";
  35         }
  36 }
  37 close IN;
  38 close OUT;
  39