[Biopython-dev] Merging the GFF3 and VCF branches

[Eric Talevich]

On Wed, Jun 10, 2015 at 2:18 AM, Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> On Tue, Jun 9, 2015 at 8:17 PM, Eric Talevich <eric.talevich at gmail.com>
> wrote:
> > On Thu, Jun 4, 2015 at 3:44 AM, Peter Cock <p.j.a.cock at googlemail.com>
> > wrote:
> >>
> >> This would be great to have merged - pathological test cases
> >> and interconversion too :)
> >>
> >> Did we settle on a plan for parent/child relationships in
> >> SeqFeature objects (beyond deprecating sub_features
> >> which has been replaced with CompoundLocations)?
> >>
> >> Peter
> >
> >
> > The last thread I see on this topic is from the end of summer 2012:
> >
> http://mailman.open-bio.org/pipermail/biopython-dev/2012-July/018979.html
> > (thread)
> >
> http://mailman.open-bio.org/pipermail/biopython-dev/2012-September/019101.html
> > (terminal)
> >
> > I'm a bit confused because the CompoundLocation class exists in
> > Bio/SeqFeature.py, and git blame says it was written in late 2011 --
> Peter's
> > Time Machine in action? Does the f_loc5 branch modify the existing
> > CompoundLocation class, then?
>
> Old commits rebased to master; perhaps a merge would have
> been clearer? As far as I recall, f_loc5 or whatever the final
> iteration of this was, is all in the master now.
>

That's great, I didn't realize this had landed already. Sorry for the
confusion.

So I suppose the remaining tasks are, in no particular order:

- Add/port Brad's GFF-GenBank converters and tests to Biopython. Ensure all
the tests pass.

- Enable GFF3 support by merging or porting from Brad's branch, bcbb/gff,
or gffutils?

- See about merging Lenna's GSoC 2012 work. This was based on the f_loc4,
not the landed f_loc5, so this won't be a clean merge. Further discussion
needed.


So I think we're ready to remove the sub_features attribute (and
> the  associated code in the GenBank parser etc which populates it).
>

Can we do that before deciding how to represent parent/child relationships?


What to add for parent/child relationships between features is
> yet to be decided.
>

I wonder if we can follow the lead of one of the GFF implementations
mentioned above.

Has this been discussed in a more recent thread that I didn't link here?

-Eric
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