[DAS] [proserver-users] GFF3 adaptor?

[Andy Jenkinson]

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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