Re: [Gmod-ajax] minimal gff

[Giles V. <gv...@sa...>]

On 15 Oct 2009, at 02:28, Mitch Skinner wrote:

> 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.
>

I completely forgot about Derives_from when I was working on it, and  
have stuck relevant upward relationships (derives_from and part_of)  
into the Parent qualifier for the time being.

> 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.
>

I do use that, but only pulling the Name, so that's fine for me.

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

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.

Regards,
Giles


> 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
>>
>>
>> -- The Wellcome Trust Sanger Institute is operated by Genome  
>> Research Limited, a charity registered in England with number  
>> 1021457 and a compa ny registered in England with number 2742969,  
>> whose registered office is 2 15 Euston Road, London, NW1 2BE. 
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart  
>> your
>> developing skills, take BlackBerry mobile applications to market  
>> and stay
>> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> http://p.sf.net/sfu/devconference
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.