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re.split fails with lookahead/behind #67006
Description
| BPO | 22817 |
|---|---|
| Nosy | @ezio-melotti, @serhiy-storchaka |
| Files |
Note: these values reflect the state of the issue at the time it was migrated and might not reflect the current state.
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GitHub fields:
assignee = None
closed_at = <Date 2015-03-02.08:59:16.402>
created_at = <Date 2014-11-07.21:42:01.324>
labels = ['expert-regex', 'type-bug']
title = 're.split fails with lookahead/behind'
updated_at = <Date 2015-03-02.08:59:16.401>
user = 'https://bugs.python.org/rexdwyer'bugs.python.org fields:
activity = <Date 2015-03-02.08:59:16.401>
actor = 'serhiy.storchaka'
assignee = 'none'
closed = True
closed_date = <Date 2015-03-02.08:59:16.402>
closer = 'serhiy.storchaka'
components = ['Regular Expressions']
creation = <Date 2014-11-07.21:42:01.324>
creator = 'rexdwyer'
dependencies = []
files = ['37147']
hgrepos = []
issue_num = 22817
keywords = ['patch']
message_count = 8.0
messages = ['230831', '230832', '230833', '230834', '230835', '230839', '230841', '237034']
nosy_count = 4.0
nosy_names = ['ezio.melotti', 'mrabarnett', 'serhiy.storchaka', 'rexdwyer']
pr_nums = []
priority = 'normal'
resolution = 'wont fix'
stage = 'resolved'
status = 'closed'
superseder = None
type = 'behavior'
url = 'https://bugs.python.org/issue22817'
versions = ['Python 3.4']
Activity
rexdwyer commentedon Nov 7, 2014
I would like to split a DNA sequence with a restriction enzyme.
A description enzyme can be describe as, e.g. r'(?<CA)(?=GCTG)'
I cannot get re.split to split on this pattern as perl 5 does.
ezio-melotti commentedon Nov 7, 2014
Can you provide a sample DNA sequence (or part of it), the exact code you used, the output you got, and what you expected?
serhiy-storchaka commentedon Nov 7, 2014
I think expected output is ['CA', 'GCTG'].
rexdwyer commentedon Nov 7, 2014
sorry if I wasn't clear.
expected output is:
acgtCA|GCTGaaacccCA|GCTGacgtacgt
-> ['ACGTCA', 'GCTGAAACCCCA', 'GCTGACGTACGT']
I would also be able to split a text on word boundaries:
re.split(r'\b', "the quick, brown fox")
-> ['the', ' ', 'quick', ', ', 'brown', ' ', 'fox']
but that doesn't work either so maybe it's a problem with all zero-width matches.
serhiy-storchaka commentedon Nov 7, 2014
This looks as one of existing issue about zero-length matches (bpo-1647489, bpo-10328).
serhiy-storchaka commentedon Nov 8, 2014
It is possible to change this behavior (see example patch). With this patch:
But unfortunately this is backward incompatible change and will likely break existing code (and breaks tests). Consider following example: re.split('(:*)', 'ab'). Currently the result is ['ab'], but with the patch it is ['', '', 'a', '', 'b', '', ''].
In third-part regex module [1] there is the V1 flag which switches incompatible bahavior change.
I don't know how to solve this issue without introducing such flag (or adding special boolean argument to re.split()).
As a workaround I suggest you to use the regex module.
[1] https://pypi.python.org/pypi/regex
serhiy-storchaka commentedon Nov 8, 2014
Previous attempts to solve this issue: bpo-852532, bpo-988761, bpo-3262.
serhiy-storchaka commentedon Mar 2, 2015
re.split() with the r'(?<CA)(?=GCTG)' pattern raises a ValueError in 3.5 (see bpo-22818). In future releases it could be changed to work with zero-width patterns (such as lookaround assertions).