my $score;
    foreach(0 .. length($string) - 1){
        my $s = substr($string, $_, 1);
        my $m = substr($shuf_seq, $_, 1);
        $score = scoring($s, $m);
        $score += $score;
        print $score;
    }
    
print "\nThis is the total mutation score: $score \n";

#sub to calculate the scoring of mutations
#If purine --> purine: -1
#If pyrimidine --> pyrimidine: -1
#If purine --> pyrimidine (or vice versa): -2
#If no change: 0
sub scoring{
    my ($a, $b) = sort @_;
   
    my %scores;
    $scores{'A'}{'G'} = -1;
    $scores{'A'}{'T'} = -2;
    $scores{'A'}{'C'} = -2;
    $scores{'G'}{'T'} = -2;
    $scores{'C'}{'G'} = -2;
    $scores{'C'}{'T'} = -1;
    $scores{'A'}{'A'} = +0;
    $scores{'T'}{'T'} = +0;
    $scores{'C'}{'C'} = +0;
    $scores{'G'}{'G'} = +0;
    
    return $scores{$a}{$b};
}