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

[Leighton Pritchard]

On 06/03/2009 15:06, "Bruce Southey" <bsouthey at gmail.com> wrote:

> Peter wrote:
>> On Fri, Mar 6, 2009 at 1:14 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
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").
>>>     
> I have already given one user case where overlapping counts is totally
> inappropriate! Unique codon counting is extremely important in many
> areas including gene prediction (possible splicing sites) and molecular
> evolution (like codon usage).

We're not discussing codon counting though, we're discussing counting
occurrences of an arbitrary substring in a sequence.  They're not the same
operation, even though they both involve counting.

L.

-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
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