[ensembl-dev] slice_adapter as MySQL procedure?

[Andy Yates]

Hi Reece,

I would urge caution as I did with Jing last week. Replicating the assembly mapper logic as a basic MySQL procedure would be impossible IMHO. You may have more luck with user defined functions but again the assembly mapper logic is not for the faint hearted. For what it is worth the Perl API isn't as slow as you may think WRT sequence retrieval especially if your requests for sequence are batched for the same region.

Best regards,

Andy

On 17 Jan 2012, at 00:18, Reece Hart wrote:

> Hi-
> 
> I'd like to be able to extract genomic sequences within MySQL itself, something like (roll dream music):
> 
> CREATE VIEW variant_context AS
> SELECT chr, start, stop, seq,
>   fetch_by_region('chromosome',chr,start-25,start-1) AS left_flank,
>   fetch_by_region('chromosome',chr,end+1,end+25) AS right_flank
> FROM variants;
> 
> Anyone ever tried to write the analog of the slice_adapter as a MySQL procedure?
> 
> Thanks,
> Reece
> 
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---
Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/