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

[Brad Chapman]

Hey all;
Great discussion on this. My preference is for a new function,
and I like Leighton's naming suggestion.

Also, unless someone has a use case for the current count()
function, we should deprecate and eventually remove it. Overriding
the string API where it makes sense is good, but here it seems to be
creating confusion and not solving a problem. If someone needs the
real string count, they can always do str(your_seq).count("GG").

Brad

> In the spirit of being blindingly obvious, how about:
> 
> Seq.overlapping_count()
> 
> ;)
> 
> L.
> 
> 
> On 06/03/2009 11:52, "Michiel de Hoon" <mjldehoon at yahoo.com> wrote:
> 
> > 
> >>> 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.
> >>> 
> >> Did you like plan (c), which preserves the Python string style count
> >> as the default but offers the non-overlapping count via an optional
> >> argument?
> >> 
> > It's also OK, but if we use a different method name we can leave count()
> > untouched altogether.
> 
> -- 
> Dr Leighton Pritchard MRSC
> D131, Plant Pathology Programme, SCRI
> Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
> e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
> gpg/pgp: 0xFEFC205C       tel:+44(0)1382 562731 x2405
> 
> 
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