[Biopython-dev] Merging the GFF3 and VCF branches

[Peter Cock]

On Wed, Jun 10, 2015 at 6:14 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:
>>
>> 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?

Yes, this can be done anytime - the SeqFeature .sub_features was
deprecated back in Biopython 1.65 so we should be fine to remove
it now as per our depreciation policy:

http://biopython.org/wiki/Deprecation_policy

>
>> 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.

An interesting question after that is if the GenBank/EMBL parser
should attempt to infer the parent/child relationships implicit in
the feature tables (e.g. gene followed by CDS feature).

Peter