[Biopython-dev] BWA Wrapper

[Peter Cock]

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