I have a script which extracts equal length DNA-sequences at user-specified positions from a genome and then calculates the frequency at which each letter (A/G/C/T) occurred at each position.

The user-specific positions can also come with a frequency - how many times that point was seen.

If this frequency is ignored (i.e. position-weighted analysis), the script runs at a satisfactory speed. However, it is when the frequencies are taken into consideration that it is considerably slow.

My approach for this has been: 

if ($mode eq "Position") {
    push (@data, $string);
} elsif ($mode eq "Freq") {
    push (@data, $string) for (1..$F[2]);
}
    
    my %freq;
for my $i (1..@data) {
    $freq{$1}[$-[0]] += 1/@data while $data[$i-1] =~ /(.)/g;
}

[download]

Which is evidently inefficient and quite literal - i.e. add that sequence X(freq) number of times into the array.

Is there a better way to do weighted frequency calculations and if so, how?

EDIT: The sequences can range from 30 to 250 characters. Weighting occurs at an average of 26, but with a range of 5-3565 for one particular sample. In any given run, around 200,000 unique positions exist within the input data.

In reply to Weighted frequency of characters in an array of strings by K_Edw

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