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

[Peter]

Brad has been working on his GFF parsing code - see progress reports
on his blog http://bcbio.wordpress.com/ and his code on github,
http://github.com/chapmanb/bcbb/tree/master/gff

Potentially this could make it into Biopython 1.51, and I was just
thinking about where the code would go.  Brad is supporting both GFF3
and the loosely defined GFF2 variants, so Bio.GFF seems a good place.
There would also be a wrapper under Bio.SeqIO for loading GFF files as
SeqRecord objects (I haven't played with Brad's code, but it can do
this already).

However, we already have a Bio.GFF module from Michael Hoffman created
back in 2002 which accesses MySQL General Feature Format (GFF)
databases created with BioPerl.  Perhaps we should poll the main
discussion list now, and if there are no responses from people using
it, we could deprecate Bio.GFF for Biopython 1.50?  Under our current
deprecation policy we shouldn't then remove Bio.GFF until Biopython
1.52 at the earliest, http://biopython.org/wiki/Deprecation_policy

What do you think Brad?  How about using Bio.GFF3 instead?

Peter