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

[Saket Choudhary]

On 28 September 2013 15:44, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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
>

Great! I had done a similar mistake while writing the samtools
wrapper(which I am yet to wrap up)
https://github.com/saketkc/biopython/commit/30b3d9878281e00afed9e7b6d0bbfb2bdacbce91

> Peter
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