Instead of setting $Chr{$key} = undef, set it to 1. Then, instead of looping through each key in the hash to find a match, you can just do a if ($Chr{$line[0]}). I only glanced over your code, so I may have missed something that would stop this from working, but there is a definite red flag when you are looping over the keys in a hash and comparing each one to some value.