/**
* Find all k-mer motifs - input dna,k,d - output
* @param array $lines
* @return array
*/
public function compute(array $lines)
{
list($k, $d) = array_map(function ($val) {
return (int) $val;
}, explode(' ', $lines[0]));
$strings = [];
$l = count($lines);
for ($i = 1; $i < $l; $i++) {
if (!empty($lines[$i])) {
array_push($strings, $lines[$i]);
}
}
$motifs = [];
for ($i = 0; $i < strlen($strings[0]) - $k + 1; $i++) {
$patt = substr($strings[0], $i, $k);
$neighbors = BioUtil::neighbors($patt, $d);
foreach ($neighbors as $nb) {
if (Arrays::matches($strings, function ($str) use($nb, $d) {
return BioUtil::approximate_frequency($str, $nb, $d, true) > 0;
}) && !Arrays::contains($motifs, $nb)) {
array_push($motifs, $nb);
}
}
}
return $motifs;
}
public static function approximate_frequency($genome, $pattern, $d, $count = false)
{
$res = $count ? 0 : [];
for ($i = 0; $i < strlen($genome) - strlen($pattern) + 1; $i++) {
$subseq = substr($genome, $i, strlen($pattern));
if (BioUtil::hamming_distance($pattern, $subseq) <= $d) {
if ($count) {
$res++;
} else {
array_push($res, $i);
}
}
}
return $res;
}