[Biopython-dev] BWA Wrapper

[Saket Choudhary]

Oops. Apparently I had forgotten to 'git add' the _bwa.py . Committed now :

https://github.com/saketkc/biopython/commit/062aabf8f31a522929957f4bcd3f7a932f3bdf23

On 16 February 2013 12:38, Saket Choudhary <saketkc at gmail.com> wrote:
> On 15 February 2013 02:08, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> On Thu, Feb 14, 2013 at 6:52 PM, Saket Choudhary <saketkc at gmail.com> wrote:
>>> In short , am I allowed to play with this extra parameter thing as per
>>> the code standards of biopython ?
>>
>> If you can come up with a nice extension to the current interface
>> for the application wrapper's __call__ method, which is backward
>> compatible, then we could be convinced.
>>
>> One idea would be stdout=True and stderr=True are treated as
>> subprocess.PIPE (as now), and a false value would continue
>> to mean don't capture the output (send it to /dev/null), but a
>> (non-empty) string argument could be interpreted as a filename
>> instead. You might be able to accept a handle, but I'm not sure
>> if all Python handles would work or not here - it requires some
>> careful cross platform testing.
>>
>> Peter
>
>
> 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