string matching with substitution using PYTHON

Question

I have a string and I need match that string with an sequence and determine the number of times the matched sequence is found in that sequence But it has following conditions Sequence can contain only ACGT valid chars so seq could be ACGTGTCTG

the string could be ACGnkG where n could be replaced by A or G k could be replaced by C or T

how can we find if the string matches the sequence by substituting valid values for n and k

Is there any regular expression ?

I have searched for various regex but not able to match as the string requires various substituitions so — Maxwell
– Maxwell, Commented Sep 5, 2012 at 0:58
Thanks so do I have to replace the char at that position with [AG] and [CT] — Maxwell
– Maxwell, Commented Sep 5, 2012 at 1:05
Do you understand how to build a regex? If not, then the regular expression HOWTO should be more helpful than trying to find a prebaked one specific to your needs. — lvc
– lvc, Commented Sep 5, 2012 at 1:28

Ansgar Wiechers · Accepted Answer · 2012-09-05 01:13:08Z

2

re.findall(pattern, string) will return a list with all matches for pattern in string. len(...) will return the number of items in a list.

answered Sep 5, 2012 at 1:13

Ansgar Wiechers

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2 Comments

jfs Over a year ago

len(lst) is wasteful for large strings such as DNA sequences

Ansgar Wiechers Over a year ago

len() will only be applied to the subset that matches the expression, so that may or may not be an issue depending on how many matches findall() returns.

jfs · Accepted Answer · 2012-09-05 01:28:30Z

1

If you want to count occurrences of the pattern:

count_regex = sum(1 for _ in re.finditer(r'ACG[AG][CT]G', s))

If you want to count occurrences of a fixed string that matches first the pattern:

m = re.search(r'ACG[AG][CT]G', s)
count_fixed = s.count(m.group(0), m.start(0)) if m else 0

answered Sep 5, 2012 at 1:28

jfs

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