[Biopython] Bio.Application now subprocess?

[Peter]

On Sat, Apr 10, 2010 at 2:58 PM, Peter wrote:
>
> OK, so you are looking at the API docs and/or the code.
> Bits of Bio/Applications.py are deprecated, and I think
> you are right - we can try and make the status clearer.
>

Hi Vincent,

I updated that a bit, hopefully it is clearer that a typical
user doesn't need to look at Bio.Applications at all.
Rather you might use the alignment tool wrappers in
Bio.Align.Applications, or the EMBOSS wrappers in
Bio.Emboss.Applications (etc) which internally use
the classes defined in Bio.Applications.

The *only* reason you'd use Bio.Applications directly
now is to write a new command line tool wrapper.

[Historically you might have used the old generic_run
function in Bio.Applications, but that is deprecated now]

Peter