[Biopython] gff3 problem

[Peter Cock]

On Tue, Apr 5, 2011 at 2:00 PM, Michal <mictadlo at gmail.com> wrote:
> Hi Peter,
> Thank you for your response. By any chance do you know how get the child
> feature like CDS and exons from the previous gff3 file?

I would guess (without having had time to really play with Brad's latest
code yet) they are in the parent feature's subfeatures list.

This is something that might change - historically the subfeatures have
been used for the GenBank/EMBL join model, whereby the exons of a
gene/CDS are held as subfeatures of the same type. There was basically
just a flat list of all the top level features. We may want to review this for
the GFF parser and perhaps introduce explicit parent child relationships
between different types (as specified in GFF3, or inferred for GenBank
or EMBL files).

Peter