How to use regex in python with varying amounts of white spaces

Question

I'm trying to turn reformat my data here:

gi|492845765|ref|WP_005999719.1| DNA methyltransferase [[Eubacterium] infirmum]

into

[[Eubacterium]infirmum]gi|492845765|

That is, I just want to just keep the gi number and the organism name (with the organism name in front of the gi number), and get rid of the "extra" information (in this case, ref number and "DNA methyltransferase").

I would do re.sub(r"(\w+ |\w + |) \w+|\w_\w|\s\w+\s\w\s ([.]), \2\1, line)

(or something remotely like that)

However, some other lines of my data have more than two words in the "extra" information. example:

gi|548229945|ref|WP_022448665.1| dNA (Cytosine-5-)-methyltransferase [Roseburia sp. CAG:303]

How would I write a regex expression to rename all of my data so that the organism name is in front, the gi numbers next, and everything else deleted?

l'L'l · Accepted Answer · 2014-02-07 23:44:01Z

2

This would probably do what you're asking:

(\w+\|\d+\|)(?:.*\s)(\[\S*)(?:\s)(.+\])

Using \2\3\1 as the replace pattern, $2$3$1 seems to work the same.

re.sub(r'(\w+\|\d+\|)(?:.*\s)(\[\S*)(?:\s)(.+\])', \2\3\1, line)

example: http://regex101.com/r/aP6lB9

edited Feb 7, 2014 at 23:44

answered Feb 6, 2014 at 22:10

l'L'l

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5 Comments

user3264659 Over a year ago

thank you very much! How would I get rid of the white space within the brackets in the 2nd group?

l'L'l Over a year ago

Ah, yes - I've updated the answer, which should take care of the spaces. :)

user3264659 Over a year ago

this one only captures the [ bracket and nothing after it. i've tried to put ([\w*)|(?:\s)| (added /w* after the front bracket) but it only finds the first word and then stops when it hits a space.

l'L'l Over a year ago

yes, sorry about that - i was in a hurry and borked it. I've updated the answer, although i think the capture is only eliminating the first space, so it might need a little more love.

user3264659 Over a year ago

Yes, it only is getting rid of the first space. But thank you very much! The regex site is very good tool, thank you for showing this to me.

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