use strict;
use warnings;

use bio::seqIO;

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

# Protein output file:
my $output_file = 'countaa';
open my $OUT, '>', $output_file
  or die "Can't open file $output_file for output.\n$!";

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

while ( my $seq = $proteinio->next_seq ) {
    foreach my $protein_seq ( $seq->seq ) {
        my %counts;
        @counts{@tracked_proteins} = ();
        my @protein = split //, $protein_seq;
        foreach my $protein_alpha (@protein) {
            next unless exists $counts{$protein_alpha};
            $counts{$protein_alpha}++;
        }
    }
    print $OUT "$_ " for @counts{@tracked_proteins};
    print $OUT "\n";
}
close $OUT or die $!;