That is absolutely possible. Some proteins do have rare amino acids such as Selenocysteine which is represented by U, etc. I'll change the regex.

Thanks for pointing out the subroutine. I was missing the print commands. Following is what I did and it worked:

sub do_something_with {

    my ($sequence,  # accumulated sequence
        $fh,        # output filehandle
        ) = @_;

    my $seq_len = length $sequence;
    my $seq_n_A = $sequence =~ tr/A//;


    printf $out_file "Number of alanines = $seq_n_A\n\n" ;
    printf $out_file "sequence length = $seq_len\n\n" ;

    }
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