#!/usr/bin/perl -w
use strict;

system "clear";
print "Palindrome - gamma version\n";
print "--------------------------\n\n";
print "Please enter DNA filename: ";

my $filename=<STDIN>;
chomp $filename;
die "No such file...exiting\n\n" unless (-e $filename);
open(DNASEQ, $filename) or die "Cannot open file...exiting\n\n";

my $last_protein;
my $count_of_2=0;
while (<DNASEQ>) {
        chomp;
        my ($lba,$rba)= ($last_protein, undef);
        for (my $lb = 0; $lb < (length) - 1; ++$lb) {
                $lba  =  substr ($_, $lb, 1);
                $rba  =  substr ($_, $lb+1, 1);
                $rba  =~ tr/atgcATGC/tacgTACG/;
                ++$count_of_2 if ($lba eq $rba);
        }
        $last_protein = $rba;
}
print "Number of 2bp palindromes: ", $count_of_2, "\n";