def patterncount_with_mismatchs(text, pattern,d):
count = 0
for i in range(0, len(text)-len(pattern)+1):
if text[i : i+len(pattern)] == pattern:
count = count + 1
elif compute_hd(text[i : i+len(pattern)],pattern) <= d:
count = count + 1
return count
def neighbors(pattern,d):
if d == 0:
return pattern
elif len(pattern) == 1:
return ["A","C","G","T"]
neighborhood = []
suffix_neighbors = neighbors(suffix(pattern),d)
for text in suffix_neighbors:
if compute_hd(suffix(pattern), text) < d:
for n in "ACGT" :
neighborhood.append(n+text)
else:
neighborhood.append(pattern[0]+text)
return neighborhood
def score(motifs,consensus):
score = 0
for motif in motifs:
score += compute_hd(motif,consensus)
return score
