How to use regular expressions in python?

Question

Hopefully someone can help, I'm trying to use a regular expression to extract something from a string that occurs after a pattern, but it's not working and I'm not sure why. The regex works fine in linux...

import re
s = "GeneID:5408878;gbkey=CDS;product=carboxynorspermidinedecarboxylase;protein_id=YP_001405731.1"
>>> x = re.search(r'(?<=protein_id=)[^;]*',s)
>>> print(x)
<_sre.SRE_Match object at 0x000000000345B7E8>

If the leading GeneID were stripped out, you could create a dict of the key/value pairs and avoid using regular expressions. dict(fragment.split("=") for fragment in s.split(';')) — user7675
– user7675, Commented Jul 7, 2013 at 12:25

TerryA · Accepted Answer · 2013-07-07 12:25:42Z

7

Use .group() on the search result to print the captured groups:

>>> print(x.group(0))
YP_001405731.1

As Martijn ~~has~~ had pointed out, you created a match object. The regular expression is correct. If it was wrong, print(x) would have printed None.

edited Jul 7, 2013 at 12:25

answered Jul 7, 2013 at 12:15

TerryA

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2 Comments

Martijn Pieters Over a year ago

That's what I get for moving out of connectivity.

TerryA Over a year ago

@MartijnPieters I gave you a mention :). I still respect you as a great pythonic master :D

Jon Clements · Accepted Answer · 2013-07-07 12:46:18Z

4

You should probably think about re-writing your regex so that you find all pairs so you don't have to muck around with specific groups and hard-coded look behinds...

import re
kv = dict(re.findall('(\w+)=([^;]+)', s))
# {'gbkey': 'CDS', 'product': 'carboxynorspermidinedecarboxylase', 'protein_id': 'YP_001405731.1'}
print kv['protein_id']
# YP_001405731.1

edited Jul 7, 2013 at 12:46

answered Jul 7, 2013 at 12:25

Jon Clements

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