Question

我尝试使用正则表达式搜索用户定义模式的核苷酸序列（仅由A，C，G，T组成）：

相关代码如下：

    match = re.match(r'{0}'.format(pattern), sequence)

match总是返回None，我需要它返回与用户查询匹配的序列部分...

我做错了什么？

编辑：这是我构建搜索模式的方式：

   askMotif = raw_input('Enter a motif to search for it in the sequence (The wildcard character ‘?’ represents any nucleotide in that position, and * represents none or many nucleotides in that position.): ')
listMotif= []    
letterlist = ['A','C','G','T', 'a', 'c','g','t']
for letter in askMotif:
    if letter in letterlist:
        a = letter.capitalize()
        listMotif.append(a)
    if letter == '?':
        listMotif.append('.')
    if letter == '*':
        listMotif.append('*?')
pattern = ''
for searcher in listMotif:
    pattern+=searcher

不是非常pythonic，我知道......

Answer 1

这应该可以正常工作：

>>> tgt='AGAGAGAGACGTACACAC'
>>> re.match(r'{}'.format('ACGT'), tgt)
>>> re.search(r'{}'.format('ACGT'), tgt)
<_sre.SRE_Match object at 0x10a5d6920>

我认为这可能是因为你的意思是使用搜索与匹配

提示您发布的代码：

prompt='''\
    Enter a motif to search for it in the sequence 
    (The wildcard character '?' represents any nucleotide in that position, 
     and * represents none or many nucleotides in that position.)
'''
pattern=None
while pattern==None:
    print prompt
    user_input=raw_input('>>> ')
    letterlist = ['A','C','G','T', '?', '*']
    user_input=user_input.upper()
    if len(user_input)>1 and all(c in letterlist for c in user_input):
        pattern=user_input.replace('?', '.').replace('*', '.*?')
    else:
        print 'Bad pattern, please try again'

Answer 2

re.match()仅在序列开头匹配。也许你需要re.search()？

>>> re.match(r'{0}'.format('bar'), 'foobar').group(0)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module> 
AttributeError: 'NoneType' object has no attribute 'group'
>>> re.search(r'{0}'.format('bar'), 'foobar').group(0)
'bar'

Python：在正则表达式中使用字符串变量作为搜索模式

2 个答案: