Any regular expressions gurus here?

[volcs0]

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.

[TheTominator]

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,/

[TheCaber]

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

[TheTominator]

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

[volcs0]

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