use 5.010;                                                                      

my $str1 = 'MALSSTAATTSSKLKLSNPPSLSHTFTASASASVSNSTSFR';

my $a_count = $str1 =~ tr/A/A/; # 6

##</code><code>##

#!/usr/bin/env perl

use 5.010;

for (<>) {
    if (/^>/) {
        # Header
    } elsif (/^[A-Z]+$/) {
        # Protein
        my $a = tr/A/A/;
        say "A: $a, length: " . length;
    }
}


##</code><code>##

open my $fh, '<', $filename
    or die "Couldn't open $filename: $!";

for (<$fh>) {