[Biopython-dev] BWA Wrapper

[Saket Choudhary]

On 18 February 2013 23:14, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> > 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
>

Thanks Peter.

I will add that. Any pointers to what would be a good reference test_aba.py
file in Tests/ directory for writing unit tests for this ?

I have worked on BDD before but Unit Tests are new for me, so it may take
some time.I plan to finish it the coming week once my university
examinations are done

Thanks

Saket