[Biopython-dev] subprocess and calling application wrappers

Peter biopython at maubp.freeserve.co.uk
Wed Jun 2 08:44:54 UTC 2010

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_utils.py

It looks complicated (and I'm sure with good reason), but I'd guess
you've never tried this on Windows?

We used to have the Bio.Application.generic_run function for calling
a command - but making the command line wrapper callable or
having a method on the command line wrapper is much easier to
use (no extra import needed).


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