[Biopython-dev] Next release plans?

Peter biopython at maubp.freeserve.co.uk
Tue Jul 28 09:17:06 UTC 2009

On Mon, Jul 27, 2009 at 11:44 PM, Brad Chapman<chapmanb at 50mail.com> wrote:
> In terms of 1.51 and beyond, I've got two things:
> - SQLite support: I'd love to push this in now for 1.51. If we have
>  a working version that people can test on, it'll encourage
>  adoption for the next BioSQL release.

I would be OK with including this once Hilmar adds the SQLite schema
to the BioSQL repository. I'd prefer him to do a point release of BioSQL
first, but as long as this is going to happen at some point that is fine.
Let's bring this up again on the BioSQL mailing list...  If Hilmar isn't
keen to rush, we *could* ship it anyway with Biopython, but it should
then be clearly labelled as a prototype schema which may be subject
to change.

> - GFF parsing: The code is revamped to be more SeqIO like based
>  on  the discussion you, Michiel and I had earlier, and the
>  documentation is in progress. I'll plan to get this in post-1.51
>  so people can work with it in git and find bugs.

Definitely post-1.51, note that EMBOSS 6.1.0 now has some support
for GFF and features in GenBank, so we can hopefully use that as a
reference implementation. i.e. Once we add GFF parsing to SeqIO,
this should let Biopython convert from GFF to SeqRecord objects to
GenBank, and we can compare this to EMBOSS.


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