Python: use string variable as search pattern in regex

Question

I'm trying to search a nucleotide sequence (composed of only A,C,G,T) for a user-defined pattern, using regex:

The relevant code is as follows:

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

match always returns None, where I need it to return the part of the sequence that matches the user query...

What am I doing wrong?

EDIT: This is how I constructed the search pattern:

   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

Not very pythonic, I know...

do you mean the sequence that i'm searching? it's really long... like more than 1000 chars — user3472351
– user3472351, Commented Apr 1, 2015 at 22:53

Josh Crozier · Accepted Answer · 2015-12-11 00:31:19Z

2

That should work fine:

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

I think it may because you mean to use search vs match

Hint on your posted code:

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'

edited Dec 11, 2015 at 0:31

Josh Crozier

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answered Apr 1, 2015 at 22:56

dawg

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1 Comment

user3472351 Over a year ago

thanks, that works. will accept your answer when stackoverflow allows me to do so :) (in six minutes for some reason)

geoelectric · Accepted Answer · 2015-04-01 22:56:34Z

1

re.match() only matches at the beginning of the sequence. Perhaps you need 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'

answered Apr 1, 2015 at 22:56

geoelectric

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