Hello

I've started using perl a couples of month ago.

I need to parse a fasta file with 2 sequences. I can read them and export in another txt without the header. Now, I need to compare both: their length, their amino acids.. but I dont know how to do that, this is my code:

my $fasta_file = "shortAligForDist.txt";
my $outfile = "Output.txt";

open OUTFILE, ">$outfile" or die "Cannot open $outfile: $!";

my $fh;
open($fh, $fasta_file) or die "can't open $fasta_file: $!\n";

my %sequence_data;
while (read_fasta_sequence($fh, \%sequence_data)) {
    #print ">$sequence_data{header}\n$sequence_data{seq}\n\n";
    print "\n$sequence_data{seq}\n\n";
    print OUTFILE "\n$sequence_data{seq}\n\n";
}

sub read_fasta_sequence {

    my ($fh, $seq_info) = @_;
    $seq_info->{seq} = undef; # clear out previous sequence

    # put the header into place
    $seq_info->{header} = $seq_info->{next_header} if $seq_info->{next_header};

    my $file_not_empty = 0;
    while (<$fh>) {
        $file_not_empty = 1;
        next if /^\s*$/;  # skip blank lines
        chomp;

        if (/^>/) { # fasta header line
            my $h = $_;
            $h =~ s/^>//;

            if ($seq_info->{header}) {
                $seq_info->{next_header} = $h;
                return $seq_info;
            }
            else { # first time through only
                $seq_info->{header} = $h;
            }
        }
        else {
            s/\s+//;  # remove any white space
            $seq_info->{seq} .= $_;
        }
    }

    if ($file_not_empty) {
       return $seq_info;
    }
    else {
        # clean everything up
        $seq_info->{header} = $seq_info->{seq} = $seq_info->{next_header} = undef;
        return;
    }
}