I may ask more questions form our Monks as I am trying to complete this script.

It ran very quick. You are right; the loops had nothing to do with the run time. A+++

Hi Jethro,

If I want to add a simple counter to count the number of lines in the output (print statement) do you know what it correct way. I pushed one of the variables into an array and counted used the scalar as a counter. But I think there should be a better way.

while(<INPUT2>){
         chomp;
          my @current_line  = split /\t/;
          push (@{$file2{$current_line[1]}}, $current_line[2]);
          if (exists $file1{$current_line[1]} ) {
               my $key = $current_line[1];
                  foreach my $position1 (@{$file1{$key}}){
          if ($current_line[1] eq $key) {
              if ($current_line[2] == $position1) {
                  if ($current_line[5] ==1) {
                      if ($current_line[14] >= 3){
               print RESULTS join ("\t", $current_line[1],$current_lin
+e[2],$current_line[5],$current_line[14], "***",$key, $position1), "\n
+";
          push (@true_positives, $current_line[1]);

                   }
                }
              }
           }
        }
    }
}
[download]

Counting needs two steps: Setting the counter to 0 before the loop and the incrementing step:

#Initialize the counter before the loop
my $true_positives=0;

while(<INPUT2>){
...

          #instead of the push
          $true_positives++;
[download]

That's it, $true_positives has the number of positive results after the loop

I think the problem lies in the 2 loops you have set up Pedro.

foreach my $position1 (@{$file1{$key}}){

This array holds the position +/- 8 that you read from the first file. Then, further down in your code, you are also adding plus/minus 8 postions from the position you read from the second file.

foreach my $pos (@range){

So I believe that is why you are getting the redundant printout.

Chris