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What regular expression can i use to match genes(in bold) in the gene list string:

GENE_LIST: F59A7.7; T25D3.3; F13B12.4; cysl-1; cysl-2; cysl-3; cysl-4; F01D4.8

I tried : GENE_List:((( \w+).(\w+));)+* but it only captures the last gene

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  • It appears that the genes are separated by semi-colons. You can use this fact to build a regex to meet your requirements. Commented Aug 11, 2016 at 18:15
  • We can help you better if you post a complete python program which you have tried. Commented Aug 11, 2016 at 18:16

4 Answers 4

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Given:

>>> s="GENE_LIST: F59A7.7; T25D3.3; F13B12.4; cysl-1; cysl-2; cysl-3; cysl-4; F01D4.8"

You can use Python string methods to do:

>>> s.split(': ')[1].split('; ')
['F59A7.7', 'T25D3.3', 'F13B12.4', 'cysl-1', 'cysl-2', 'cysl-3', 'cysl-4', 'F01D4.8']

For a regex:

(?<=[:;]\s)([^\s;]+)

Demo

Or, in Python:

>>> re.findall(r'(?<=[:;]\s)([^\s;]+)', s)
['F59A7.7', 'T25D3.3', 'F13B12.4', 'cysl-1', 'cysl-2', 'cysl-3', 'cysl-4', 'F01D4.8']
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5 Comments

In my case i am searching through a large xml file to find gene information, so i actually need to search for "Gene_list" first and then try to pull each gene out to add it to the list of all genes
Have you considered using an XML parser such as ElementTree?
Yes, i am actually using it, however gene information is not stored as a node of its own, it is listed in the node "notes" which has a lot of other information(other than the gene names) that i am not currently concerned about
This is more what i was looking for: (?<=[(GENE_LIST):;]\s)([^\s;]+)
@SeanSadykoff: The regex (?<=[(GENE_LIST):;]\s)([^\s;]+) is not what you think. With the [] around [(GENE_LIST):;] you are looking for the individual characters of the string GENE_LIST which is functionally no different than the regex (?<=[:;]\s)([^\s;]+) in this case. If you want to add the string to the lookback, you would do something like (?<=(?:^GENE_LIST: )|(?:; ))([^\s;]+) or just eliminate the lookback and use (?:(?:^GENE_LIST: )|(?:; ))([^\s;]+)
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You can use the following:

\s([^;\s]+)

Demo

  • The captured group, ([^;\s]+), will contain the desired substrings followed by whitespace (\s)
>>> s = 'GENE_LIST: F59A7.7; T25D3.3; F13B12.4; cysl-1; cysl-2; cysl-3; cysl-4; F01D4.8'
>>> re.findall(r'\s([^;\s]+)', s)
['F59A7.7', 'T25D3.3', 'F13B12.4', 'cysl-1', 'cysl-2', 'cysl-3', 'cysl-4', 'F01D4.8']
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7 Comments

this will capture the whitespace in front too, so the first gene capture would be ' F59A7.7'
@RubenPirotte i am not sure if there are multiple whitespaces before each one anyway updated..
I'm sorry, I think you misunderstood: the \s captures the whitespace, while we only want the gene behind that whitespace.
so either a trim should be done, or the regex has to be modified.
@RubenPirotte Did you check the modified answer?
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UPDATE

It's in fact much simpler:

[^\s;]+

however, first use substring to take only the part you need (the genes, without GENELIST )

demo: regex demo

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2 Comments

Yes, the last gene is not followed by a semicolon
is the last gene always preceded by a space?
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string = "GENE_LIST: F59A7.7; T25D3.3; F13B12.4; cysl-1; cysl-2; cysl-3; cysl-4; F01D4.8"
re.findall(r"([^;\s]+)(?:;|$)", string)

The output is:

['F59A7.7',
'T25D3.3',
'F13B12.4',
'cysl-1',
'cysl-2',
'cysl-3',
'cysl-4',
'F01D4.8']
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