On Apr 28, 6:30 am, Nick Craig-Wood <[EMAIL PROTECTED]> wrote:
> 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
Thank you! Your suggestion was overly helpful.
Also thank you for the package suggestions. BioPython is on my plate
to check out, but I needed a kind of quick fix for this one. The
documentation for biopython seems pretty thick - I'm not a biologist
so I'm not even sure what kind of packages I'm even looking for.
thanks!
Blaine
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