[DAS] [proserver-users] GFF3 adaptor?

[Dan Bolser]

I was thinking about the ID=, Name=, and Alias= tags in column 9.
However, to be honest I'm not sure if/how you'd want to plumb those
tags into DAS queries/responses!

Just getting ahead of myself really!


Cheers,
Dan.

On 7 January 2013 13:51, Andy Jenkinson <andy.jenkinson at ebi.ac.uk> wrote:
> Hi Dan,
>
> I doubt the old CVS repo has a gff3 dedicated adapter.
>
> Not too familiar with BioPerl's GFF3 support, what does it give you, besides a sequential parser? What you need to be able to do is index by location for fast random access, either with an index file or in memory. The parent/part stuff does add a layer of complexity. I had plans to write one some time ago but didn't work on it much.
>
> Cheers,
> Andy
>
> On 7 Jan 2013, at 13:25, Dan Bolser <dbolser at ebi.ac.uk> wrote:
>
>> Sorry, I omitted to mention that this is using ProServer.
>>
>> On 7 January 2013 13:25, Dan Bolser <dbolser at ebi.ac.uk> wrote:
>>> Hi,
>>>
>>> Has anyone written a dedicated GFF3 adaptor? Getting GFF3 via the file
>>> adaptor seems a bit of a hack, especially as BioPerl has good GFF3
>>> support.
>>>
>>> I read that "Customised extensions are also still available in the old
>>> CVS repository." Could that be where the GFF3 adaptor is maintained?
>>>
>>> Would be good to add this to the SVN if anyone has one :-)
>>>
>>>
>>> Cheers,
>>> Dan.
>>
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>