def approx_pat_posi(pattern, text, d):
posilist = []
lenp = len(pattern)
lent = len(text)
d = int(d)
for i in xrange(lent - lenp + 1):
if hamming_dist(text[i:i + lenp], pattern) <= d:
posilist.append(str(i))
return ' '.join(posilist)
def approx_pat_posi(pattern, text, d):
posilist = []
lenp = len(pattern)
lent = len(text)
d = int(d)
for i in xrange(lent - lenp + 1):
if hamming_dist(text[i:i + lenp], pattern) <= d:
posilist.append(str(i))
return ' '.join(posilist)
def maxfreq_mm(seq, k, d):
k = int(k)
d = int(d)
seql = len(seq)
freq_dict = defaultdict(int)
for kmer in permutdna(k):
for i in xrange(seql - k + 1):
if hamming_dist(kmer, seq[i:i + k]) <= d:
freq_dict[kmer] += 1
maxfreq = max(freq_dict.values())
for kmer in freq_dict:
if freq_dict[kmer] == maxfreq:
print kmer,