Re: [Gmod-ajax] minimal gff

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

I was talking about this thread:

http://www.nabble.com/getting-JBrowse-to-run-off-a-Chado-database-where-feature.name-field-is-not-used-td25491225.html

That thread ended a little inconclusively, I thought; Scott had 
suggested a database change ("set feature.name = feature.uniquename") 
and then Giles started working on genedb->gff->jbrowse rather than 
straight genedb->jbrowse.  And then performance became an issue; it 
sounds like Giles solved it in his case, but in general I hope to avoid 
making people do as much work as he has done.

Part of the reason I was thinking about having an sql-to-json.pl (that 
would take an sql query as a parameter) is this site-specific variation 
in chado usage.  I'm not sure how much of it there is, though.

Other reasons were:
* allowing other kinds of queries than the ones supported by Bio::DasI
* not having to write Bio::DB::Das::UCSC (unless someone has already 
written this?)
* not having the bio object intermediate (when I profiled a BED->json 
conversion, the biggest CPU user was Bio::Root::RootI::_rearrange)

On the other hand, you could argue (as Chris Mungall did to me today) 
that it would be better to work on improving the middleware rather than 
trying to avoid it.  And then there's the reasons that people have 
wanted middleware in the past (not writing m*n mappings between m data 
sources and n consumers, but m+n mappings to/from the middleware).  I 
think that would be an interesting discussion to have; each of those m*n 
mappings can be simpler than the mappings to and from the middleware, 
and also take advantage of unique features of the source and destination.

Mitch

Scott Cain wrote:
> Hi Mitch and Giles,
>
> I must have missed the conversation about Bio::DB::Das::Chado; what
> were the nature of the problems?  I can't say I'm terribly surprised
> that there were problems, since GeneDB has been using Chado for a long
> time and so Chado and the gbrowse adaptor have no doubt evolved away
> from the way GeneDB is using it.
>
> Anyway, is there anything I can do?
>
> Scott
>
>
> On Thu, Oct 15, 2009 at 7:21 PM, Mitch Skinner
> <mit...@be...> wrote:
>   
>> 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
>>
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