Well, just to show the Power of Perl, you could replace the entire contents of your foreach(my $protein=$seq->seq){ loop with:

  my %count;
  $count{$_}++ for map uc, split '', $protein;

  for ( 'A' .. 'Z' ) {
    say RESULT "$_: ", $count{$_} / length $protein if $count{$_};
  }
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