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

[Peter]

Hi all,

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 want to suggest we deprecate Michael Hoffman's Bio.GFF module
in Biopython 1.53 (I'm hoping we can do this next month, Dec 2009).
Depending on how soon Brad's code is ready to be merged (which I
am assuming could be Biopython 1.54, spring 2010), we can perhaps
accelerate removal of the old module.

How does that sound? If we're all happy on the dev list, we'll still
need to ask on the main list in case if anyone is using the old
Bio.GFF code.

Peter