[Biopython-dev] [Bug 2779] Seq.count() docstring should note unexpected behaviour

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2779





------- Comment #8 from barwil at gmail.com  2009-03-05 07:58 EST -------
(In reply to comment #4)

> This could probably be done more efficiently.  Is something like this already
> implemented in Bio.Motif
> 

In Bio.Motif you can do:

m=Bio.Motif.Motif()
m.add_instance(Seq("GG"),m.alphabet))
for i in m.search_instances(Seq("GGGG",m.alphabet)):
  print i

this should give you overlapping hits

there is Bio.Motif in CVS, but the same implementation is in Bio.AlignAce.Motif
(now obsoleted).


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