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

[Brad Chapman]

Peter;
Thanks for the plug. GFF parsing is moving along; the main feature
two things I would like to finish before proposing it for inclusion
are writing of GFF files and putting GFF into BioSQL with the nested
features. The code does work for parsing, and I've been using it for
some real projects; anyone who would like to test it is more than
welcome.

As far as the current Bio.GFF, that is a bit of a conundrum. The
current code does work and for some cases it would be nice of having
the utility of working with GFF from a database. Eventually BioSQL
from GFF may supplant that, but that should be finished and tested
first. I would argue for keeping it in.

However, it is a bit confusing if someone is looking for a parser. It
would make more sense if it lived under a namespace like Bio.GFF.DB.
What do you think about adding a warning that it is going to move to
a new namespace and then moving it there, if we don't hear any
complaints, for 1.51? This is less cumbersome than a removal for
users since it's just an import change.

Brad



> 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
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