Nobody has spotted the obvious, that the code for reading the file is painfully slow.
A significant improvement would be:
while (read($fh, my $char, 1) && $eof) {
if ($char =~ m/[ACGT]/ ) {
$i++;
if ($i >= $start_genome && $i < $end_genome) {
push (@genome, $char);
} elsif ($i > $end_genome) {
$eof = 0;
# do the searching here, instead of outside the loop!
}
}
}
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