[Biopython-dev] Merging the GFF3 and VCF branches

[Lenna Peterson]

On Wed, Jun 10, 2015 at 1:14 PM, Eric Talevich <eric.talevich at gmail.com>
wrote:

> 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.
>

Fortunately, it's based on f_loc5 and should merge cleanly. I just rebased
it today; my PR is still active.
https://github.com/biopython/biopython/pull/309


>
>
> 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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