Regular expression to extract string between two words

Question

I have a string without space.

ATG AGC TAA CTC AGG TGA TGG GGA ATG CCC CGC TAA

I need to extract string between ATG and ending with either TAG|TGA|TAA (should not include the end) . How do I extract from the string to get

ATGAGC and ATGCCCCGCTAA using regular expressions.

what I have tried

pattern = re.compile(r'(?=(ATG(?:...)*?)(?=TAG|TGA|TAA))')

it does not work as expected.

I feel like this same questions gets asked around this time every year.... For instance [here](http://stackoverflow.com/q/18731894/) and [here](http://stackoverflow.com/q/16260794/) and [here](http://stackoverflow.com/q/19761908/) and [here](http://stackoverflow.com/q/31757876) and.... — Dan, Sep 18 '16 at 04:46
@Dan - Haha. Perhaps you could link to the search page instead — OneCricketeer, Sep 18 '16 at 04:52
@cricket_007 probably all I need to do is link to a search for the tags [tag:regex] AND [tag:python] AND [tag:bioinformatics] and every question would be some variation of regex patterns for genome patterns. I'd need to exclude the [tag:pandas] tag, though. — Dan, Sep 18 '16 at 04:54

score 1 · Accepted Answer · answered Sep 18 '16 at 04:46

1

Use following regex:

In [14]: regex = re.compile(r'(ATG.*?)(?:TAG|TGA|TAA)')

In [15]: regex.findall(s)
Out[15]: ['ATGAGC', 'ATGGGGAATGCCCCGC']

Note that these matches are not contain the trailing.

answered Sep 18 '16 at 04:46

Mazdak

score 0 · Answer 2 · answered Sep 18 '16 at 04:53

0

import re

pattern = re.compile(r'(ATG[A-Z]+)(?:TAG|TGA|TAA)')
results = pattern.search('ATGCCCCGCTAA')

print results.groups(0)

Results in

('ATGCCCCGC',)

answered Sep 18 '16 at 04:53

Soviut

score 0 · Answer 3 · answered Sep 18 '16 at 07:26

This works, given that endings are not included:

>>> re.findall(r'(ATG(?:...)*?)(?:TAG|TGA|TAA)', seq)
['ATGAGC', 'ATGCCCCGC']

?: means that patterns will not be captured in the result.

...: specifies exactly three characters. Alternative are .{3} or the more restrictive case of [ACTG]{3}

*?: implies minimum match. Without this, longest match will be obtained.

3 Answers3