I have a large set (100000+) of short DNA reads 20 characters long.
I need to compares all reads against each other and pull out those that vary by just 1 position. Heres the script I came up with.
$| = 1;
my $compare_count = 0;
for (my $i = 0; $i < @kmers; $i++ ) {
for (my $j = $i + 1; $j < @kmers; $j++ ) {
print "\rComparing sequence $i to $j";
my @result = PCCompare::dissimilarity($kmers[$i], $kmers[$j],
+1);
if ($result[0] == 1) {
print "\rMatch found: $kmers[$i], $kmers[$j]\n";
push @variant_kmers, ($kmers[$i], $kmers[$j]);
}
$compare_count++;
}
}
print "\rFinished: $compare_count comparisions made.\n";
The problem is that this loop runs very very slow.
It takes on the orders of days to process 100000 sequences.
Is there a way to make the process faster?
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