[BioPython] The count method of a Seq (or MutableSeq) object

[Michiel de Hoon]

I vote (b).
Another option is to continue to use count() for a Python-style count, and to add a new method that does a overlapping-type count. For this new method we'd need a clear but short name, and I can't think of anything now.

--Michiel.


--- On Thu, 3/5/09, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: [BioPython] The count method of a Seq (or MutableSeq) object
> To: "BioPython Mailing List" <biopython at lists.open-bio.org>
> Date: Thursday, March 5, 2009, 7:26 AM
> Hi All,
> 
> As the following examples show, and the python string
> method's
> docstring clearly states, the python string's count
> method uses a
> non-overlapping search:
> 
> >>> "AAA".count("A")
> 3
> >>> "AAA".count("AA") # you
> might expect 2
> 1
> >>> "BBBB".count("BB") # you
> might expect 3
> 2
> 
> Up until Biopython 1.44, the Seq object's count method
> only worked for
> single characters.  From Biopython 1.45 onwards it accepted
> longer
> strings and followed the built in python string count
> behaviour.
> However, as Noel pointed out on Bug 2779 our docstring does
> not make
> it clear that this does a non-overlapping search.  In fact,
> as
> Leighton suggests, one might the Seq object to use an
> overlapping
> search in the Seq object's count method.
> http://bugzilla.open-bio.org/show_bug.cgi?id=2779
> 
> We should either:
> 
> (a) stick with the python string compatible behaviour
> (which has been
> a general principle for the Seq class), but document this
> issue more
> clearly as a non-overlapping search does run counter to
> some potential
> biological uses.
> 
> or,
> 
> (b) Or change the behaviour as Leighton suggests to do an
> overlapping
> search.  This could break any code relying on the old
> python
> string-like behaviour.
> 
> What do people here think?  Any preferences?
> 
> [I don't want to get into details about the
> implementation here on the
> main list]
> 
> Peter
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