[Biopython-dev] BWA Wrapper

[Peter Cock]

> On 16 February 2013 12:38, Saket Choudhary <saketkc at gmail.com> wrote:
>> HI Everyone,
>>
>> I have pushed the wrapper to
>> https://github.com/saketkc/biopython/tree/bwa_wrapper
>>
>> Should I send a pull request ? I am in the middle of my University
>> mid-semester examinations and hence this is not completely tested. I
>> need to perform some more tests with more parameters after I am done
>> with my examinations the next week.
>>
>>
>> I would like to hear comments or have it code-reviewed, since this is
>> the first time I am contributing to biopython and I might have missed
>> out on some of the coding practices being followed.
>>
>> Thanks
>>
>> Saket


On Sat, Feb 16, 2013 at 11:48 AM, Saket Choudhary <saketkc at gmail.com> wrote:
> Oops. Apparently I had forgotten to 'git add' the _bwa.py . Committed now :
>
> https://github.com/saketkc/biopython/commit/062aabf8f31a522929957f4bcd3f7a932f3bdf23
>

This looks sensible. I think if we are going to extend the __call__ interface
to allow stdout to be a filename, then we should do the same for stderr
as well. Also this needs to be explained in the docstring (and perhaps
also the Tutorial somewhere).

Separately some simple unit tests for the wrapper would be good too
(which can be as much work as the original code itself), and would
be beneficial for cross-platform testing.

Thanks,

Peter