[Biopython-dev] Fwd: Where to put command line wrappers

[Peter]

On Fri, Apr 17, 2009 at 3:02 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>
>> I can see that Bio.Application.generic_run function is often handy,
>> but sometimes it is quite inappropriate.  For AlignAce obviously it
>> has sufficed.
>
> Yeah, generic_run is not as generic as it should be. It does have a
> lot of hard fought logic for working with multiple python versions
> and windows/unix. Could we make generic_run appropriate for the big
> standard out cases so we don't end up duplicating that in
> Blast/Clustalw/wherever runners?

The AlignAce and Clustalw already call generic_run internally - and
for them it is fine.  For BLAST, by default the output goes to
standard out, so generic run is a bad idea as this loads all of stdout
into memory.  We may want to add some variations on generic_run for
this kind of usage, or say it is up to the user to deal with it as
appropriate for their setup.

Peter