def percent_match(seq1, seq2):
# list formatted as [max-number-complementary, index, index, index]
# print "percent_match \nreturns the percentage of complementarity between two strings of bases\n"
# assume both strings are passed '3 --> '5'
# reverse one string for binding
seq_helpers.reverse(seq1)
len1 = len(seq1)
len2 = len(seq2)
num_matches = 0
num_comped = 0
p1 = len1 - 1
p2 = 0
while p2 < len2:
num_matches += substring_match(seq1[p1:], seq2[p2:])
num_comped += len(seq1[p1:])
if p1 > 0:
p1 = -1
else:
p2 += 1
return (num_matches * 1.0) / num_comped
def find_binding_sites(seq1, seq2):
seq_helpers.reverse(seq1)
len1 = len(seq1)
len2 = len(seq2)
max_val = 0
num_matches = {}
p1 = len1 - 1
p2 = 0
matches = 0
while p2 < len2:
matches = substring_match(seq1[p1:], seq2[p2:])
if matches in num_matches:
num_matches[matches] += (p1, p2)
else:
num_matches[matches] = (p1, p2)
if p1 > 0:
p1 -= 1
else:
p2 += 1
max_val = max(num_matches.keys())
return [max_val, num_matches[max_val]]