Ok, now I'm more confused than ever and chasing my tail in frustration. This is where I am with the code. Any helpful suggestions are appreciated. 

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

#use strict;
use warnings;
use File::Slurp;
use Data::Dumper;
my @data;
my @col;
my $dataset;
my @fields;
#my %out;
my $Hashref;
my $fileCount;
my @out; 
my @results;

open INFILE, "<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;
     }
    }


while (<INFILE>){

        @col = split(/\t+/, $_);
        chomp (@col);
         my ($header, $length, $tm, $sequence) = @col[0..3];

        # expecting file3 line in @col

        my @results = ( $col[1], $col[2] );

#print Dumper (\@results)
}

for my $dataset (@data) {
    my @out = push @{
    $data[ $fileCount ]->{
        shift @col
    }
},  \@col;



#print Dumper (\@data);
}

    @out = 
        sort {
            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;
          }   @out;

print Dumper (\@out);

    push @results, $out[0]->[2];

#print Dumper (\@results);
#}

[download]

In reply to Re^14: Combining 3 files by garyboyd
in thread Combining 3 files by garyboyd

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.