Curious Curious - 4 months ago 22
Python Question

python regular expression. Extract text between patterns

How to get all the values in between 'uniprotkb:' and '(gene name)' in the 'str' below:

str = 'uniprotkb:HIST1H3D(gene name)|uniprotkb:HIST1H3A(gene name)|uniprotkb:HIST1H3B(gene name)|uniprotkb:HIST1H3C(gene name)|uniprotkb:HIST1H3E(gene name)|uniprotkb:HIST1H3F(gene name)|uniprotkb:HIST1H3G(gene name)|uniprotkb:HIST1H3H(gene name)|uniprotkb:HIST1H3I(gene name)|uniprotkb:HIST1H3J(gene name)'


The result is:

HIST1H3D
HIST1H3A
HIST1H3B
HIST1H3C
HIST1H3E
HIST1H3F
HIST1H3G
HIST1H3H
HIST1H3I
HIST1H3J

Answer

Using re.findall(), you can get all parts of a string that match a regular expression:

>>> import re
>>> sstr = 'uniprotkb:HIST1H3D(gene name)|uniprotkb:HIST1H3A(gene name)|uniprotkb:HIST1H3B(gene name)|uniprotkb:HIST1H3C(gene name)|uniprotkb:HIST1H3E(gene name)|uniprotkb:HIST1H3F(gene name)|uniprotkb:HIST1H3G(gene name)|uniprotkb:HIST1H3H(gene name)|uniprotkb:HIST1H3I(gene name)|uniprotkb:HIST1H3J(gene name)' 
>>> re.findall(r'uniprotkb:([^(]*)\(gene name\)', sstr)

['HIST1H3D', 'HIST1H3A', 'HIST1H3B', 'HIST1H3C', 'HIST1H3E', 'HIST1H3F', 'HIST1H3G', 'HIST1H3H', 'HIST1H3I', 'HIST1H3J']
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