Bioinformatics - Scoring DNA mutations

allsop_5 has asked for the wisdom of the Perl Monks concerning the following question:

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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Re: Bioinformatics - Scoring DNA mutations
by Athanasius (Archbishop) on Apr 30, 2016 at 07:23 UTC

Hello allsop_5, and welcome to the Monastery!

The code as given is imcomplete, as it doesn’t show the declaration and initialization of the variables $string and $shuf_seq. It would be useful if you could provide sample values for these variables, together with the final $score value you expect to generate from these sample values.

One point stands out: in these lines:

$score = scoring($s, $m);
$score += $score;
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you first overwrite the value of the variable $score, then add this new value to itself (thereby doubling it). Neither of these is what you intend. You need something along these lines:

my $score;

foreach (...)
{
    ...
    my $local_score = scoring($s, $m);
    $score += $local_score;
    print $local_score;    # (or did you want to print $score here?)
}
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And BTW: you do begin your script with:

use strict;
use warnings;
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don’t you?

Hope that helps,

Athanasius <°(((>< contra mundum Iustus alius egestas vitae, eros Piratica,

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Re: Bioinformatics - Scoring DNA mutations
by graff (Chancellor) on Apr 30, 2016 at 15:44 UTC

my @arr = ( -10, -5, -1, 0, 2, 6, 11 );

# mimicking to the OP code:
for my $n ( @arr ) {
    print $n;
}

# being more detail-oriented:
for my $n ( @arr ) {
    print "$n\n";   # include a newline after the value
}
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