Hi all, I'm doing an assignment that requires I shuffle a DNA sequence, then score the "mutations" according to a set of rules. I have come up with the below code and it is obviously not working (gives really odd results, like -2-4-400-200...etc) I'm hoping I just did something silly. My intent was to create a foreach loop that would use the subroutine I have that has a hash that creates numeric values based on evaluating the keys (hopefully that makes sense). Here is the code:

 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};
}

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In reply to Bioinformatics - Scoring DNA mutations by allsop_5

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