Re: [Gmod-ajax] minimal gff

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

This is cool, sorry for the slow reply on my part.  I wasn't sure about 
"Derives_from" that you mentioned in your first email.  I'm not aware of 
any reason jbrowse would use that, but I don't know the 
Bio::DB::SeqFeature::Store code in detail, which would be the place to 
look to answer this question definitively.

Also, if the user is using the "extraData" jbrowse option, then whatever 
is being extracted from the perl objects that way would be relevant, 
although I suppose the user already knows if that's the case.

Out of curiosity, are you generating GFF from a chado database, or is it 
another schema?

Regards,
Mitch

On 10/14/2009 04:19 PM, Giles Velarde wrote:
> Further to this question I decided to investigate. Adapting the SQL 
> code from one of the Chado views (gff3view), to generate a custom 
> mini-GFF exporter without any annotations. A typical set of lines 
> looks like this:
>
> Lbr.chr1 chado gene 1272 4166 . - . ID=3775871;Name=LbrM01_V2.0010
> Lbr.chr1 chado exon 1272 4166 . - . 
> ID=3775872;Name=LbrM01_V2.0010:exon:1;Parent=LbrM01_V2.0010:mRNA
> Lbr.chr1 chado mRNA 1272 4166 . - . 
> ID=3775873;Name=LbrM01_V2.0010:mRNA;Parent=LbrM01_V2.0010
>
> and JBrowse appears to handle this fine for my purposes. I haven't 
> done any benchmarks, but it's significantly faster than exporting the 
> complete GFF. In terms of size alone I am it's gone from 60M to 36M 
> for the same dataset.
>
> If anyone would like to know more on this topic please feel free to 
> get in touch.
>
> Regards,
> Giles
>
>
>
>
> On 14 Oct 2009, at 16:48, Giles Velarde wrote:
>
>> Hi,
>>
>> I am looking to possibly speed up the generation of GFFs for 
>> consumption by the JBrowse prepare scripts, and wanted to check with 
>> you first to see what attributes (tags in the last column) are 
>> absolutely necessary for JBbrowse. I am guessing :
>>
>> - ID
>> - Name
>> - Parent
>> - Derives_from
>>
>> would that be correct?
>>
>> Regards,
>> Giles
>
>
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