def close_enough_old(self, primer, sequence, errors) :
err_count = 0
for i,j in zip(sequence, primer) :
if not IUPAC.equal(i, j) :
err_count += 1
#if len(a) > 10 :
# print a, b, err_count
return err_count <= errors
def close_enough(self, primer, sequence, diff) :
if diff < 0 :
return False
if (len(primer) == 0) or (len(sequence) == 0) :
return True
m = IUPAC.equal(sequence[0], primer[0])
return self.close_enough(primer[1:], sequence[1:], diff if m else diff-1) or \
self.close_enough(primer[1:], sequence, diff-1) or \
self.close_enough(primer, sequence[1:], diff-1)
def distance(self, aligned) :
leng = float(min(len(aligned[0]), len(aligned[1])))
last_gap = True
diff = 0
for c1,c2 in zip(aligned[0], aligned[1]) :
if (c1 == '-') and (c2 == '-') :
continue
gap = '-' in (c1,c2)
if last_gap and gap :
continue
if not IUPAC.equal(c1, c2) :
diff += 1
last_gap = gap
if last_gap :
diff -= 1
return (leng - diff) / leng
