open my $out_file, '>', 'aa_report.txt' or die "Cannot open 'aa_report.txt' because: $!";

print 'PLEASE ENTER THE FILENAME OF THE PROTEIN SEQUENCE: ';
chomp( my $prot_filename = <STDIN> );

open my $PROTFILE, '<', $prot_filename or die "Cannot open '$prot_filename' because: $!";

$/ = ''; # Set paragraph mode

while ( my $para = <$PROTFILE> ) {
    # Remove fasta header line
    $para =~ s/^>.*//m;
    # Remove comment line(s)
    $para =~ s/^\s*#.*//mg;

    my %prot;
    $para =~ s/([A-Z])/ ++$prot{ $1 } /eg;

    print $out_file join( ' ', map "$_=$prot{$_}", sort keys %prot ), "\n";
    }