def getSignature2(host, readPath, writePath, count):
'''
用smith waterman算法对请求进行序列比对，找到最合适的子序列，
经过加工，生成签名
'''
sig = []
filePath = readPath + '/' + host + '/'
if os.path.exists(filePath):
files = os.listdir(filePath)
for file in files:
sample = []
with open(filePath + file, 'rb') as f:
lines = f.readlines()
for line in lines:
line = line.decode('utf-8').strip()
sample.append(line)
if len(sample) > count:
dis = int(len(sample) / count)
sample = sample[::dis]
if len(sample) > 1:
symbol = alignment.water(sample[0], sample[1])
for i in range(2, len(sample)):
symbol = alignment.water(symbol, sample[i])
'''
tokens=st.GetTokenList(sample)
signature=st.GetSignature(tokens)
'''
symbol = symbol.replace(' ', '(.*)')
wildcard = '(.*)?'
signature = ''
signatureSplit = symbol.split('(.*)')
for s in signatureSplit:
if s != '':
signature += wildcard
signature += '('
signature += re.escape(s)
signature += ')'
signature += wildcard
sig.append(signature)
sig = list(set(sig))
sig.sort(key=lambda x: len(x))
if len(sig) > 0:
filePath = writePath + '/' + host
with open(filePath, 'wb') as f:
for s in sig:
s = s.encode('utf-8')
f.write(s)
f.write('\n'.encode('utf-8'))
def check_duplicates(self, tweet1, tweet2):
tweet1 = tweet1.lower().split()
tweet2 = tweet2.lower().split()
self.match_len = alignment.water(tweet1, tweet2)
if self.match_len >= self.threshold:
return True
else:
return False
#!/usr/bin/env python import sys, string import alignment # Command-line arguments '''f1 = open(sys.argv[1], 'r') seq1 = f1.readline() seq1 = string.strip(seq1) f2 = open(sys.argv[2], 'r') seq2 = f2.readline() seq2 = string.strip(seq2) ''' seq1 = 'asdef' seq2 = 'nibla' alignment.water(seq1, seq2)
def pair_merge(self, loga, logb):
loga, logb = alignment.water(loga.log_split(), logb.log_split())
logn = []
for idx, value in enumerate(loga):
logn.append('<*>' if value != logb[idx] else value)
return " ".join(logn)
from alignment import needle, water
# from msa import main
from fasta import getFasta
id = ["B5CZ00", "B5CZ01", "B5CZ02"]
seq = []
for i in id:
seq.append(getFasta(i))
if len(id) == 2:
needle(seq[0], seq[1])
water(seq[0], seq[1])
else:
exit()