[Biopython-dev] Merging the GFF3 and VCF branches

[Brad Chapman]

Eric and Peter;
Thanks again for moving this forward. cc'ing in Ryan as well, in case he
hasn't seen this discussion.

> 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.

I'd suggest moving those scripts to use gffutils, rather than rely on
bcbb/gff. Ryan's implementation is better and I'd prefer to deprecate
mine and move forward with his work.

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

My vote is for gffutils.

> 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?

I lost this as well so am not sure the best starting place. I don't have
a strong opinion and open to doing whatever y'all think is best.

Thanks again,
Brad