[Biopython-dev] Implementation of Application interface

[Brad Chapman]

Hello all;
I thought this might be of interest to Davide and others interested
in accessing applications through Biopython.

We talked a while back about a generic interface for specifying
command lines and running programs through biopython, in a thread
starting here:

http://www.biopython.org/pipermail/biopython-dev/2001-August/000476.html

Well, I've been working in biopython-corba on implementing
interfaces to remote programs (through Novella,
http://industry.ebi.ac.uk/novella/) and wrote up a "biopython-like"
interface that implements what we were talking about.

The code for this is in biopython-corba CVS in
BioCorba/Bio/Application/__init__.py, and on-line here (sorry 'bout
the long URL):

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython-corba/BioCorba/Bio/Application/__init__.py?rev=1.1&content-type=text/vnd.viewcvs-markup&cvsroot=biopython
                    
Anyways, I thought a working implementation of what we talked about
might be of interest to people, and once we
get the generic application stuff working in biopython, we can
synchronize these interfaces so the biopython-corba stuff models as
closely as possible the biopython code.

Comments on whether I accurately implemented what we talked about,
etc, are very welcome.

Brad
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