[Biopython-dev] ApplicationResult and generic_run obsolete?

Brad Chapman chapmanb at 50mail.com
Mon Jul 6 22:04:53 UTC 2009

Hi all;

> > this object gets used in the function generic_run. So we'd have to
> > obsolete that too. [If anyone can see any other side effects of
> > deprecating Bio.Application.ApplicationResult please speak up]
> I'm fine with deprecating ApplicationReslut.

Bartek, you just won the typo of the month contest hands down.

> > If we want to deprecate Bio.Application.generic_run (in order to
> > deprecate Bio.Application.ApplicationResult), then do we need a
> > replacement? Or replacements?
> > However, I'm tempted to say Biopython shouldn't be duplicating basic
> > Python functionality, like wrapping the subprocess module in helper
> > functions for typical situations. Instead we should just document
> > using the current recommend Python best practice (which I believe to
> > be use the subprocess module). The downside is that using subprocess
> > is a bit tricky for novices.

My vote is to document using subprocess and avoid creating our own
wrapper. No one has to learn a Biopython specific API for running
programs, and subprocess provides plenty of flexibility to get stdout,
stderr and return codes. For places where we feel like using subprocess
is tricky, additional documentation within Biopython should help those
encountering it for the first time. This gives us more time to work
on biology problems, and leaves the running programs problems up to
the greater Python community.


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