This precisely answered my question. John, Thanks!
• 0 views
•
link
written
by
jinkuozhang •
Why my regular expression fails to match all the reasonable seq?
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:
- ACAATTGTAGTATATAAAAA (13, 36)
- 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?
• 1,914 views
•
link
updated
by
John
•
written
by
jinkuozhang •
•
written
by
jinkuozhang •
1 answer
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)
If this answered your question it's appropriate to mark this answer as "accepted".
• 0 views
•
link
written
by
WouterDeCoster
Log in to answer this question.