Why my regular expression fails to match all the reasonable seq?

Question

[jinkuozhang]

I try to find all the possible "N20NGG" sequence in a target sequnce like:

example_seq ATTAATACTTTTAACAATTGTAGTATATAAAAAAGGGAGTAACCGAAAACGGTCGGGACCGAAAACGG

What I used is python regular expression:

import re
example_seq = "ATTAATACTTTTAACAATTGTAGTATATAAAAAAGGGAGTAACCGAAAACGGTCGGGACCGAAAACGG"
pattern = re.compile(r'(.{20}).GG')
all_matched_seq = pattern.finditer(example_seq)

for record in all_matched_seq:
    print(record.group(1), end="\t")
    print(record.span())

I ony got two matched sequences:

1. ACAATTGTAGTATATAAAAA (13, 36)
2. AAAACGGTCGGGACCGAAAA (45, 68)

My script failed to retrieve the other 4 matched sequences:

CAATTGTAGTATATAAAAAA; AAAAAGGGAGTAACCGAAAA; AGGGAGTAACCGAAAACGGT; GGGAGTAACCGAAAACGGTC;

How can I modify my script to get all the reasonable ones?

Answer 1

[John]

Regex's by default in python are non-overlapping. You have to use the lookahead operator ?=

import re
example_seq = 'ATTAATACTTTTAACAATTGTAGTATATAAAAAAGGGAGTAACCGAAAACGGTCGGGACCGAAAACGG'
pattern = re.compile(r'(?=((.{21})GG))')
all_matched_seq = pattern.finditer(example_seq)
for record in all_matched_seq:
    print(record.group(1), end="\t")
    print(record.span())

ACAATTGTAGTATATAAAAAAGG (13, 13)
CAATTGTAGTATATAAAAAAGGG (14, 14)
AAAAAGGGAGTAACCGAAAACGG (29, 29)
AGGGAGTAACCGAAAACGGTCGG (33, 33)
GGGAGTAACCGAAAACGGTCGGG (34, 34)
AAAACGGTCGGGACCGAAAACGG (45, 45)
  

[jinkuozhang]

This precisely answered my question. John, Thanks!

[WouterDeCoster]

If this answered your question it's appropriate to mark this answer as "accepted".