[Biopython-dev] [Bug 2779] Seq.count() docstring should note unexpected behaviour
bugzilla-daemon at portal.open-bio.org
bugzilla-daemon at portal.open-bio.org
Thu Mar 5 12:58:40 UTC 2009
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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