blaine <[EMAIL PROTECTED]> wrote:
> I'm trying to write a string matching algorithm for genomic
> sequences. I'm pulling out Genes from a large genomic pattern, with
> certain start and stop codons on either side. This is simple
> enough... for example:
>
> start = AUG stop=AGG
> BBBBBBAUGWWWWWWAGGBBBBBB
>
> So I obviously want to pull out AUGWWWWWWAGG (and all other matches).
> This works great with my current regular expression.
>
> The problem, however, is that codons come in sets of 3 bases. So
> there are actually three different 'frames' I could be using. For
> example:
> ABCDEFGHIJ
> I could have ABC DEF GHI or BCD EFG HIJ or CDE FGH IJx.... etc.
>
> So finally, my question. How can I represent this in a regular
> expression? :) This is what I'd like to do:
> (Find all groups of any three characters) (Find a start codon) (find
> any other codons) (Find an end codon)
>
> Is this possible? It seems that I'd want to do something like this: (\w
> \w\w)+(AUG)(\s)(AGG)(\s)* - where \w\w\w matches EXACTLY all sets of
> three non-whitespace characters, followed by AUG \s AGG, and then
> anything else.
I'm not sure what the \s are doing in there - there doesn't appear to
be any whitespace in your examples.
> I hope I am making sense. Obviously, however, this will make sure
> that ANY set of three characters exist before a start codon. Is
> there a way to match exactly, to say something like 'Find all sets
> of three, then AUG and AGG, etc.'.
I think you want
^(\w\w\w)*(AUG)((\w\w\w)*?)(AGG)
which will match up 0 or more triples, match AUG match 0 or more triples
then AGG. The ? makes it a minimum match otherwise you'll match more
than you expect if there are two AUG...AGG sequences in a given genome.
>>> import re
>>> m=re.compile(r"^(\w\w\w)*(AUG)((\w\w\w)*?)(AGG)")
>>> m.search("BBBBBBAUGWWWWWWAGGBBBBBB").groups()
('BBB', 'AUG', 'WWWWWW', 'WWW', 'AGG')
>>> m.search("BBBQBBBAUGWWWWWWAGGBBBBBB")
>>> m.search("BBBQQBBBAUGWWWWWWAGGBBBBBB")
>>> m.search("BBBQQBBQBAUGWWWWWWAGGBBBBBB")
<_sre.SRE_Match object at 0xb7de33e0>
>>> m.search("BBBQQBBQBAUGWWWWWWAGGBBBBBB").groups()
('BQB', 'AUG', 'WWWWWW', 'WWW', 'AGG')
>>> m.search("BBBQQBBQBAUGWQWWWWWAGGBBBBBB")
>>> m.search("BBBQQBBQBAUGWWWWQWWAGGBBBBBB")
>>> m.search("BBBQQBBQBAUGWWQWWQWWAGGBBBBBB")
>>> m.search("BBBQQBBQBAUGWWQWAWQWWAGGBBBBBB")
<_sre.SRE_Match object at 0xb7de33e0>
>>> m.search("BBBQQBBQBAUGWWQWAWQWWAGGBBBBBB").groups()
('BQB', 'AUG', 'WWQWAWQWW', 'QWW', 'AGG')
>>>
> This way, I could scan for genes, remove the first letter, scan for
> more genes, remove the first letter again, and scan for more genes.
> This would hypothetically yield different genes, since the frame
> would be shifted.
Of you could just unconstrain the first match and it will do them all
at once :-
(AUG)((\w\w\w)*?)(AGG)
You could run this with re.findall, but beware that this will only
return non-overlapping matches which may not be what you want.
I'm not sure re's are the best tool for the job, but they should give
you a quick idea of what the answers might be.
--
Nick Craig-Wood <[EMAIL PROTECTED]> -- http://www.craig-wood.com/nick
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