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

[Michiel de Hoon]

Hi Brad,

Thanks for your work on the GFF parser; I'm dealing with GFF files quite a lot. Could you maybe give a simple example of how to use your GFF parser, once it's included into Biopython?

--Michiel.


--- On Mon, 4/6/09, Brad Chapman <chapmanb at 50mail.com> wrote:

> From: Brad Chapman <chapmanb at 50mail.com>
> Subject: Re: [Biopython-dev] Bio.GFF and Brad's code
> To: biopython-dev at lists.open-bio.org
> Date: Monday, April 6, 2009, 6:08 PM
> 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
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at lists.open-bio.org
> >
> http://lists.open-bio.org/mailman/listinfo/biopython-dev
> _______________________________________________
> Biopython-dev mailing list
> Biopython-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython-dev