Regular Expression - Matching Multiples of 3 Characters exactly.

[blaine]

On Apr 28, 6:30 am, Nick Craig-Wood <n... at craig-wood.com> wrote:
> blaine <frik... at gmail.com> 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 <n... at craig-wood.com> --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