First of all, please post your code together with your problem. The Monks usually help fixing problems, not write your scripts for you.

Depending on the amount of data, you may use a hash to preload the data:

for my $nr (1..2) {
 for my $line (read_file('file'.$nr)) {
  my @cols = split(/\t/,$line);
  push @{$data[$nr - 1]->{shift(@cols)}},\@cols;
 }
}
[download]

This code reads both file1 and file2 (outer for loop) line by line (inner for loop), splits the lines into columns and stores the data in a tree referenced by file number and contig*-key (first column). It's using File::Slurp and I suggest that you look at the tree using Data::Dumper.

Next, compare it to your third file. Given you read and splitted the file already using a while (<$fh>) loop or using read_file:

# expecting file3 line in @col
my @results = ($col[0],$col[3]);
for my $dataset (@data) {
 push @results,(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 <=> $diff_b;
  } @{$dataset->{$col[0]}})[0]->[2];
}
[download]

This block sorts the preloaded data sets using the difference to the comparison value of the current row and adds the alpha-key to the @result list which has been preloaded with the key and the file3 alpha string.
You could easily print out the @result data tab-delimited using join().

This is no complete script, but the code samples should give you an idea how to handle your data, merging them is now easy.

If you got too much data to reasonable load it into memory, think about using a database (maybe SQLite) to handle the problem, it might be better than a pure perl solution.

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]

Hmmm...still struggling with this one and getting an error :

Can't use an undefined value as an ARRAY reference at combine_primer_lists.pl line 42, <INFILE> line 1.

relating to this line:

    } @{$dataset->{$col[0]}})[0]->[2];

Could you explain what this line is doing?

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

use strict;
use warnings;
use File::Slurp;
use Data::Dumper;
my @data;
my @col;
my @dataset;
my $a;
my $b;
my @fields;
my %out;

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) {
         push @results,(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 <=> $diff_b;
          } @{$dataset->{$col[0]}})[0]->[2];
        }
}
[download]

That is easy, the line is confusing :)

It is also confusing $dataset for a hashref

perltidy

my @results = ( $col[0], $col[3] );
for my $dataset (@data) {
    push @results, (
        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;
          } @{ $dataset->{ $col[0] } }
    )[0]->[2];
}
[download]

is like

my @results = ( $col[0], $col[3] );
for my $dataset (@data) {
    my ( $first ) = 
        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;
          } @{ $dataset->{ $col[0] } }

    push @results, $first->[2];
}
[download]

is like

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];
}
[download]

$a and $b are globals, they're how sort works

Is it still confusing?

See what I said here Re^3: How-To integrate information from two hash tables? :)