[BioPython] More string methods for the Seq object

[Leighton Pritchard]

+1 for following the Python default.

A less straightforward implementation might use a knowledge of the Alphabet
for the Seq to strip out non-Alphabet characters, such as gaps, but I think
that this, along with (a) and (c), would be overkill.  I like the principle
of least surprise in this case.

On 29/09/2008 12:50, "Peter" <biopython at maubp.freeserve.co.uk> wrote:

>>> No one has objected to adding strip and split (plus lstrip and rstrip)
>>> so if we take that as a consensus, the only point we should still
>>> debate is their default arguments.  Other alternatives to what I have
>>> already put forward include following the python string and defaulting
>>> to white space (which would never normally be present in a sequence),
>>> or making the arguments non optional.
> 
> Listing out those explicitly, for the poposed Seq object methods:
> (a) strip, lstrip and rstrip default to the gap character.  split
> argument is mandatory.
> (b) strip, lstrip, rstrip and split all default to white space
> (following string default)
> (c) strip, lstrip, rstrip and split all have a mandatory argument
> (explicit better than implicit)
> 
>> I do agree especially in terms of attempting to keep the standard
>> Python defaults and behavior.
> 
> I assume you are agreeing with what I have now called (b), follow the
> string defaults of white space for stipping or splitting (for
> consistency, even though this won't typically be useful for
> sequences).  On balance this would probably be best from a principle
> of consistency and least surprise for the user - I'll update the
> patches.
> 
> Peter


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