[Biopython-dev] subprocess and calling application wrappers

[Jose Blanca]

On Wednesday 02 June 2010 10:44:54 Peter wrote:
> On Wed, Jun 2, 2010 at 7:21 AM, Jose Blanca <jblanca at btc.upv.es> wrote:
> > On Tuesday 01 June 2010 17:15:03 Peter wrote:
> >> On Tue, Jun 1, 2010 at 2:23 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
> >> > Peter;
> >> >
> >> >> With the new command line wrappers and the tutorial pushing
> >> >> users towards using subprocess we've had more queries
> >> >> about how to use it. The subprocess module itself is rather
> >> >> scary I guess, and things could be made a lot easier.
> >
> > We had the same need. We solved it with a call function. You can take
> > a look at:
> >
> > http://github.com/JoseBlanca/franklin/blob/master/franklin/utils/cmd_util
> >s.py
>
> It looks complicated (and I'm sure with good reason), but I'd guess
> you've never tried this on Windows?

Yes it is somewhat complicated. We need some functionalities like accepting 
stdout to be a file or just a pipe (some programs have very long stdouts). We 
have added everything we have required for our programs.

No, we haven't test anything on windows.

-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)