[Biopython-dev] Adjusting the xxMotif wrapper / Bio.Application plans

[Peter Cock]

On Thu, Aug 8, 2013 at 11:37 AM, Christian Brueffer
<christian at brueffer.de> wrote:
>>
>> Was there a special reason for all these case variants
>> in the XXmotif options??
>
> I basically followed the example set by
> Bio/Align/Applications/_Clustalw.py.

Ah. Without checking I think maybe the ClustalW documentation
used both cases - but the order was deliberately with the lower
case one last as that was used in the Python object as the
property name and keyword.

> The "rationale" was to allow for people to use their favourite
> spelling variety.
>
> I guess it was bad luck this happened to serve as an example, as it
> was the first piece of code I ever touched in BioPython.
>
> It would be nice to streamline all application wrappers in this regard
> sometime...

Yeah, perhaps we can formally deprecate set_parameter in
the next release which means all the aliases 'go away' and
that leaves us with just the final entry exposed as the usable
property name and keyword.

Peter