Thanks again for your help. Would you mind explaining how this section is working?

 # now remove double counted patients from the data structure
foreach my $gene ( values %site_length_catch) {
        for my $count ( values %$gene ) {
                $count = keys %$count; # in scalar context you get the
+ number of keys
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I get that you've created a hash of a hash of a hash $site_length_catch{$gene}{$sit}{$patient} = 1; and initialized the bottom value array to 1 ...correct? but then with this part how are you accessing the values of the next level... why would you use  values %site_length_catch instead of keys %site_length_catch

Thanks again for your time, the code works great, I just want to fully understand whats happening.