[Biopython-dev] BWA Wrapper

[Saket Choudhary]

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