Re: [Gmod-ajax] minimal gff

[Mitch S. <mit...@be...>]

Giles Velarde wrote:
> Yes I am using this to pull data out of GeneDB here at Sanger, which 
> is a Chado database. I have put it up here : 
>
> http://github.com/gv1/chado2miniGFF
>
> It's mostly SQLs, inside light Python wrapper. 
>
> We usually use Artemis to bulk-export GFF, but in this case we don't 
> need all the annotations for the time being, and even if we do  use 
> some in the future ( for use in extraData) the approach would be to 
> selectively put them in. 

Given the difficulty you had with Bio::DB::Das::Chado, and given that 
I'd like to be able to generate jbrowse json from the UCSC database 
(and, potentially, other databases) I've been kicking around the idea of 
having something like an sql-to-json.pl.  You could give it a database 
connection and an sql query (and probably some perl callbacks for 
munging the results) and it would generate jbrowse json for you.

Simple cases would be really easy; the jbrowse json is already sort of 
tabular.  I'm not sure yet about how to deal with subfeatures though, 
given that different databases deal with those quite differently.

FWIW,
Mitch