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]

Ok, now I'm more confused than ever and chasing my tail in frustration.

You still have

my @out = push @{
    $data[ $fileCount ]->{
...
[download]

Why?

Thanks anonymous monk!!! I now have a breakthrough!!! I think it helped me to sleep on things as well!

So I removed the:

 my @out = push @{
    $data[ $fileCount ]->{
...
[download]

and now have :

#!/usr/bin/perl
#29/06/2011

#use strict;
use warnings;
use File::Slurp;
use Data::Dumper;
my @data, my @col, my @fields;
my $dataset;
#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[0], $col[3] );
for my $dataset (@data) {
    my @beef = @{ $dataset->{ $col[0] } };
    @beef = 
        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;
          }   @beef;

    push @results, $beef[0]->[2];
#print Dumper (\@results);

 foreach (@results){
            print $_."\n";}
 
}
}
[download]

I checked the output from @results and it is almost there generating the output. There are however strange things going on.

output looks like:

contig03841
CCAGGTTATTTATTTCAGCGGGAACT
AGTAGTTCATAATAAAGAGGAGGCTGGT
contig03841
CCAGGTTATTTATTTCAGCGGGAACT
AGTAGTTCATAATAAAGAGGAGGCTGGT
AGTAGTTCATAATAAAGAGGAGGCTGGA
contig06486
GCAAATGGCTCTAAGGATCAGCC
TTTTCCTGAGCGTTTTCCTGAGC
contig06486
GCAAATGGCTCTAAGGATCAGCC
TTTTCCTGAGCGTTTTCCTGAGC
CATTTTTCCTGAGCGTTTTCCTGAGT
contig09294
GTCGGAGCTCTCTCAGAACCC
GCCCCAGAAGACATCACCTTCAT
contig09294
GTCGGAGCTCTCTCAGAACCC
GCCCCAGAAGACATCACCTTCAT

contig100253
CACTCGAGTTGCAGTTATGTTCCTC
AGATGATTTGTGCATTATAATTGTAATTTGGGC
contig100253
CACTCGAGTTGCAGTTATGTTCCTC
AGATGATTTGTGCATTATAATTGTAATTTGGGC
GAGATGATTTGTGCATTATAATTGTAATTTGGGT
[download]

I think the gaps are where there are entries missing from the files. Is there a way to print out only those results in @results where there is data from all 3 input files? eg it will output

contig100253
CACTCGAGTTGCAGTTATGTTCCTC
AGATGATTTGTGCATTATAATTGTAATTTGGGC
GAGATGATTTGTGCATTATAATTGTAATTTGGGT
[download]

rather than......

contig100253
CACTCGAGTTGCAGTTATGTTCCTC
AGATGATTTGTGCATTATAATTGTAATTTGGGC
contig100253
CACTCGAGTTGCAGTTATGTTCCTC
AGATGATTTGTGCATTATAATTGTAATTTGGGC
GAGATGATTTGTGCATTATAATTGTAATTTGGGT
[download]

I also want to output the data on one line tab-delimited, so for example

contig100253 AGATGATTTGTGCATTATAATTGTAATTTGGGC GAGATGATTTGTGCATTATAATTGTAATTTGGGT CACTCGAGTTGCAGTTATGTTCCTC