BTW:

foreach (my ($key, $value) = each %linked_counts_by_abbr){
    print OUTPUT "$key => $value\n";
    }
[download]

I would be surprised if this loop does what you think and hope it does. Iteration over a hash with each is usually implemented with a  while loop (see perlsyn for  while loop info).

>perl -wMstrict -le
"my %hash = qw(a 1 b 2 c 3 d 4);
 print 'foreach loop output:';
 foreach (my ($k, $v) = each %hash) {
   print qq{$k => $v};
   }
 print 'while loop output:';
 keys %hash;
 while (my ($k, $v) = each %hash) {
   print qq{$k => $v};
   }
"
foreach loop output:
c => 3
c => 3
while loop output:
c => 3
a => 1
b => 2
d => 4
[download]

(PS: Does anyone know why the OP is rendering so strangely?)