[Biopython-dev] Bio.GFF and Brad's code

[Peter]

On Wed, Dec 2, 2009 at 12:57 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
> Hi Peter;
>
>> Brad has some GFF parsing code he as been working on, which
>> would be nice to merge into Biopython at some point. See:
>>
>> http://lists.open-bio.org/pipermail/biopython-dev/2009-April/005700.html
>>
>> As we started to discuss earlier this year, we need to think about
>> what to do with the existing (old) Bio.GFF module. This was written
>> by Michael Hoffman back in 2002 which accesses MySQL General
>> Feature Format (GFF) databases created with BioPerl.
>>
>> I've been looking at the old Bio.GFF code, and there are a lot of
>> redundant things like its own GenBank/EMBL location parsing,
>> plus its own location objects and its own Feature objects (rather
>> than reusing Bio.SeqFeature which should have sufficed).
>
> I'm ambivalent on deprecating GFF. Agreed that some of it is not
> well integrated with the rest of Biopython, with the
> Location/LocationFromString code being the most duplicated. It's too
> bad feature were reimplemented as well. Is Michael around at all?

I got in touch with Michael Hoffman - he has moved from the EBI to
the University of Washington but his EBI email address still worked.
He said:

"Please feel free to deprecate the module or make any
necessary changes for the project."

Even if you (Brad) didn't have a new GFF parser waiting to be
added to Biopython, I would still want to do something with
Bio.GFF to reduce the redundancy of location and feature code.
Deprecation is the simplest solution (but I may be able to
reuse some of his location string parsing code on Bug 2738).

Peter