def frequent_words_with_mismatch(text, kmers, d):
count_dict = dict()
max_count = 0
visited_kmers = set()
for kmer in kmers:
app = approx_pattern_count(text, kmer, d) + approx_pattern_count(text, reverse_dna(kmer), d)
if app > 0 and kmer not in visited_kmers:
if kmer not in count_dict:
count_dict[kmer] = 0
count_dict[kmer] += app
if count_dict[kmer] > max_count:
max_count = count_dict[kmer]
result = [key for key in count_dict if count_dict[key] == max_count]
return result, max_count
def frequent_words_with_mismatch(text, kmers, d):
count_dict = dict()
max_count = 0
visited_kmers = set()
for kmer in kmers:
app = approx_pattern_count(text, kmer, d) + approx_pattern_count(
text, reverse_dna(kmer), d)
if app > 0 and kmer not in visited_kmers:
if kmer not in count_dict:
count_dict[kmer] = 0
count_dict[kmer] += app
if count_dict[kmer] > max_count:
max_count = count_dict[kmer]
result = [key for key in count_dict if count_dict[key] == max_count]
return result, max_count
table = {}
reverse_table = {}
for line in f.readlines():
gens, acid = line.split()
if acid == '""':
acid = ''
table[gens] = acid
if acid not in reverse_table:
reverse_table[acid] = [gens]
else:
reverse_table[acid].append(gens)
reverse_table[''].append('')
stuff = []
# stuff.append(reverse_table[''])
for letter in pattern:
stuff.append(reverse_table[letter])
# stuff.append(reverse_table[''])
result = []
# text = text.replace('T', 'U')
for candidate in itertools.product(*stuff):
string = ''.join(candidate)
string = string.replace('U', 'T')
if string in text:
result.append(string)
string = reverse_dna(string)
if string in text:
result.append(string)
with open('out.txt', 'w') as f:
f.write('\n'.join(result))
"""
index = 0 - len(sub)
try:
while True:
index = string.index(sub, index + len(sub))
yield index
except ValueError:
pass
def get_kmers(s, k):
return list(set(["".join(x) for x in window(s, k)]))
if __name__ == '__main__':
with open('in.txt', 'r') as f:
k = int(f.readline())
s1 = f.readline().strip()
s2 = f.readline().strip()
possible_kmers = get_kmers(s1, k)
result = list()
for kmer in possible_kmers:
for first_pos in find_all(kmer, s1):
for second_pos in find_all(kmer, s2):
result.append((first_pos, second_pos))
for second_pos in find_all(reverse_dna(kmer), s2):
result.append((first_pos, second_pos))
with open('out.txt', 'w') as f:
f.write(str('\n'.join(map(str, result))))
