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#!/usr/bin/env python
import sys, os
binding = { 'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C', '_': False }
def max_consecutive_binding(mer1, mer2):
if len(mer2) > len(mer1):
mer1, mer2 = mer2, mer1
# save the len because it'll change when we do a ljust
mer1_len = len(mer1)
# reverse mer2,
mer2 = mer2[::-1]
# pad mer one to avoid errors
mer1 = mer1.ljust(mer1_len + len(mer2), "_")
max_bind = 0;
for offset in range(mer1_len):
consecutive = 0
for x in range(len(mer2)):
if binding[mer1[offset+x]] == mer2[x]:
consecutive = consecutive + 1
else:
consecutive = 0
max_bind = max(consecutive,max_bind)
return max_bind
def test():
# mer 1 mer 2 # correct ans
arr = [
("ATATAT", "TATATA", 5),
("ACAGGGAT", "ATATATAT", 2),
("CATATATAT", "ATATATATATAT", 8),
("ATATATATATAT", "ATATATATAT", 10),
("ATATAT", "TATAT", 5),
("AACGATACCATG", "GGATCATACGTA", 3),
("CGT", "ACG", 3),
("ACG", "CGT", 3),
("CACC", "GGTGT", 4),
("GGTGT", "CACC", 4),
("CCCCCCCCATATAT", "TATA", 4),
]
print 'pass\tmer1\tmer2\tres\tcorr'
for mer_combination in arr:
response = []
ans = max_consecutive_binding(mer_combination[0], mer_combination[1])
response.append(str(ans == mer_combination[2]))
response.append(mer_combination[0])
response.append(mer_combination[1])
response.append(str(ans))
response.append(str(mer_combination[2]))
print '\t'.join(response)
def main():
if(len(sys.argv) < 2):
print "cutoff is expected as an argument"
exit()
else:
cutoff = int(sys.argv[1])
for line in sys.stdin:
mer = line.split()[0]
if max_consecutive_binding(mer, mer) < cutoff:
sys.stdout.write(line)
if __name__ == "__main__":
sys.exit(main())
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