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

[Peter Cock]

On Thu, Aug 8, 2013 at 12:00 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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

I have updated the application wrapper code to spot hyphens
in what should be property names/arguments:
https://github.com/biopython/biopython/commit/ba1a43475a3d4450b3ac8409adaf0e59a25b0e47

This forced me to update the XXmotif wrapper and I opted
to switch it to using lower case property names:
https://github.com/biopython/biopython/commit/f4b4006a64d5166b5c0934d2ad1f8dc3bab30067

I was looking at this as part of applying Christian's MSAProb wrapper:
https://github.com/biopython/biopython/pull/225

Peter