[BioSQL-l] Plone4bio 1.0 and BioSQL

[Peter]

Thanks for the report James!

On Thu, Oct 1, 2009 at 2:20 PM, James Procter <jimp at compbio.dundee.ac.uk> wrote:
>
> * issue #2: The imagemap shown under the 'Features' tab is generated using
> bioperl from a genbank file emitted by biopython. This is a flaw, and means
> lots of info is lost (my biosql db is used to serve protein
> sequence DAS annotation, so it has URLs, scores, and lots of notes).

That is a curious and round about way of doing things, with many
data transformations risking loosing things at each point.

It would be possible to use Biopython's GenomeDiagram module to
draw the image directly (although the style and capabilities would
differ). I've done this for an in house TurboGears based BioSQL
front end, and it was fine for prokaryotic organisms.

Another more elegant alternative would be to call a BioPerl script which
talks to the BioSQL database directly to get the data to draw the image.

Can you point me at the relevant files in Plone4bio to see their code?
I agree with your general point that a pluggable rendering option might
be best, but that would be a question for the Plone4bio team to debate.

Peter
[Biopython Project]