this code fails to count the dipeptides globally. gives count less than the actual value. Unable to figure it out...anyone plese help......thanks in advance

 
#!/usr/bin/perl

use strict;
use warnings;
use List::Util qw(sum);

print "Please type the filename of the DNA sequence MMta: ";
my $file = <STDIN>;
chomp $file;
# Use three arg open and test for errors
open my $fh_in, '<', $file or die "Unable to open '$file': $!";

my %count;
my $seq;
# loop on every lines of input file
while(my $line = <$fh_in>) {
    chomp $line;
    # Find the sequence name
    $seq = $1 if $line =~ /(>.*?cds)/;
    # Count
    while($line =~ /(AA|AL|DA|DE|DV|VD|DW|QD|SD|HD|ED|DY|VE|EN|EI|KE|N
+V|VP|FV|SS|WK|KK)/ig) {
        $count{$seq}{$1}++;
    }
}

open my $fh_out, '>', 'countbase.txt' or die "Unable to open 'countbas
+e.txt': $!";
# Display the result separately for each sequence
foreach(keys %count) {
    my $sum = sum(values %{$count{$_}});
    my $abs = 22 - scalar keys %{$count{$_}};
    print $fh_out $_,"\nsum = ",$sum,"\nabs = ", $abs,"\n";

}

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In reply to how do i count the 22 selected di-peptides from a multifasta file separately for each sequence by SOMEN

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