+- MacResource (https://forums.macresource.com)
+-- Forum: My Category (https://forums.macresource.com/forumdisplay.php?fid=1)
+--- Forum: Tips and Deals (https://forums.macresource.com/forumdisplay.php?fid=3)
+--- Thread: Any regular expressions gurus here? (/showthread.php?tid=69260)
Any regular expressions gurus here? - volcs0 - 12-29-2008
I want to take a string (a protein sequence) and replace all the instances of "K*" and "R*" (where * is anything) with "K,*" and "R,*" respectively. In other words, every time a K or an R appears, I want to place a comma after it. The exception is any time there is a P following the K or R - then no insert. This is how the enzyme trypsin acts. I'm trying to do this in python, but I'm not very good at regular expressions.
I could iterate through the sequences, but I think regex will be much faster.
For instance:
MVLTIYPDELVQIVSDKIASNRGKITLNQLWDISGKPFDLSDKKVKQFVLSCVILKKDI
MVLTIYPDELVQIVSDK,IASNR,GK,ITLNQLWDISGKPFDLSDK,K,VK,QFVLSCVILK,K,DI
Any help is appreciated. I will keep reading and post back if I figure it out.
Thanks.
Re: Any regular expressions gurus here? - TheTominator - 12-29-2008
How about this one?
I'm not sure how Python does regexps. This should be suitable for Perl-alikes.
s/([KR])[^P]/\1,/
If I got the memory part of the replacement expression wrong, you can do it in two passes with
s/K[^P]/K,/
s/R[^P]/R,/
Re: Any regular expressions gurus here? - TheCaber - 12-29-2008
TheTominator wrote:
How about this one?
I'm not sure how Python does regexps. This should be suitable for Perl-alikes.
s/([KR])[^P]/\1,/
...
s/([KR])([^P])/\1,\2/
will not strip off the non-P following a K-or-R match
Re: Any regular expressions gurus here? - TheTominator - 12-29-2008
TheCaber wrote:
[quote=TheTominator]
How about this one?
I'm not sure how Python does regexps. This should be suitable for Perl-alikes.
s/([KR])[^P]/\1,/
...
s/([KR])([^P])/\1,\2/
will not strip off the non-P following a K-or-R match
Oh yeah. Good catch.
I always do programming in two stages.
Stage 1: Bugging
Stage 2: Debugging
Re: Any regular expressions gurus here? - volcs0 - 12-30-2008
Thanks.
This is the python code that did it. I could not do it in one pass. There is no global flag for python for regex.
def trypsinize(proteins):
p = re.compile(r'([K|R])([^P])'
q = re.compile(r'([K|R])([^,P])'
output = []
for protein in proteins:
name = protein[0]
sequence = protein[1]
a = p.sub(r'\1,\2',sequence)
b = q.sub(r'\1,\2',a)
output.append([name,b.split(','])
return output