Thanks for your help its most appreciated. I understand the first block of code, but I'm not sure I fully understand the second block in the while (<$fh3>) loop. Could you explain in more detail?

I have been playing around with the script and Data::Dumper and I get an error message:

Use of uninitialized value in hash element at combine_primer_lists.pl line 41, <$fh3> line 1.

Can't use an undefined value as an ARRAY reference at combine_primer_lists.pl line 46, <$fh3> line 1.

 #!/usr/bin/perl
#22/06/2011

# Usage: perl combine_primer_lists.pl

use strict;
use warnings;
use File::Slurp;
use Data::Dumper;
my @data;
my @col;
my %dataset;

#open my $fh1, "<Primer-For1" or die $!;
#open my $fh2, "<Primer-For2" or die $!;
open (my $fh3, '<', "Primer-Rev1") or die $!;
open my $outfh, '>', "outputfile.txt" or die $!;


for my $nr (1..2) {
 for my $line (read_file('Primer-For'.$nr)) {
  my @col = split(/\t/,$line);
  push @{$data[$nr - 1]->{shift(@col)}},\@col;
#print Dumper(\$nr);
#print Dumper (\@col);

 }
}


while (<$fh3>){

#print Dumper (\$fh3);

        # expecting file3 line in @col
        my @results = ($col[0],$col[3]);
        for my $dataset (@data) {
#print Dumper (\@data)
         push @results,(sort {
#print Dumper (\@results)
           my $diff_a = $col[2] - $a->[1];
           $diff_a *= -1 if $diff_a < 0;
          my $diff_b = $col[2] - $b->[1];
           $diff_b *= -1 if $diff_b < 0;
           $diff_a <=> $diff_b;
          } @{$dataset->{$col[0]}})[0]->[2];

    }
}
[download]