Here is a solution to counting the letters taken from the BioPerl webpage, the 'HOWTO:Beginners' link on the opening page, then link 17 - (Obtaining basic sequence statistics). That led to the docs on Bio::Tools::SeqStats.

#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
use Bio::Tools::SeqStats;

my @prot = qw/ A C D E F G H I K L M N P Q R S T V W Y /;

my $outputfile = "countaa";
open my $OUT, ">", $outputfile
    or die "Can't open file \"$outputfile\" to write to $!\n\n";

my $proteinio=Bio::SeqIO->new (-file=>"ec 1.1.1.fasta",-format=>'fasta
+');

while(my $seq = $proteinio->next_seq() ) {
    my $seq_stats = Bio::Tools::SeqStats->new(-seq => $seq);
    my $count = $seq_stats->count_monomers();
    print $OUT join(' ', map {$_ || 0} @$count{ @prot }), "\n";
}

close $OUT or die $!;
[download]

Hope this is of some help,

Chris