[Biopython-dev] Bio.GFF and Brad's code

[Peter]

Hi Jose,

On Tue, Jan 26, 2010 at 2:02 PM, Jose Blanca <jblanca at btc.upv.es> wrote:
> Hi:
>
> I'm doing a pipeline to annotate sequences. I'm writting modules that add
> SeqFeatures and annoations to the sequences.

I've done a little of that too - but with GenBank files as the output.

> Right now I'm storing the result as repr for the SeqRecords, but I would like
> to write gff files at the end. I've read the discussion regarding Brad's code
> and I've found it very interesting.
> I need to write those gff files so couldl use Brad's code or my own, but it
> would be great if I could contribute to Biopython at the same time.
> At the time being I don't think a consensus about what a SeqFeature should
> represent and how. I think Peter made a proposal about adding a parent and
> children properties, is this a good way to solve the problem?
> Best regards,

Brad's code is using the SeqFeature differently to existing bits of
Biopython, and adding a separate child/parent mechanism for the
kind of usage required for GFF(3) looks like one way forward allowing
use to keep full backward compatibility. I'm actually going to see Brad
in person next month at a workshop, and I'm hoping we can squeeze
in a little in person debate on this then (assuming we don't settle it
here on the mailing list first of course).

Regards,

Peter