[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 #4 from lpritc at scri.sari.ac.uk  2009-03-05 05:16 EST -------
Created an attachment (id=1255)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1255&action=view)
Patch to Seq.py that modified count behaviour for Seq and MutableSeq objects to
return correct counts for substrings of length > 1

(In reply to comment #3)
> Thanks for the workaround but could you replace the current count by that code?

I don't have access to CVS ;)

It would be nice to get consensus that the behaviour that this code would
produce is the desired behaviour for everyone, that we've got an acceptable way
of implementing it, and that it doesn't break anything downstream.  There's
bound to be, at best, a lag time.

I've attached a proposed patch based on the above code, though it's not
necessarily the best way to solve this problem.

> Can you imagine any existing code that would break because of correction of
> buggy behaviour?

That should come out in the testing.

And it turns out that there is a Bio.Motif, but it's in CVS. D'oh! again...


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