[ensembl-dev] database access

Dan Staines dstaines at ebi.ac.uk
Thu Mar 14 14:45:55 GMT 2013

On 03/14/2013 02:34 PM, Gary Duncan wrote:
> It supposed to pull the dicty introns and it just pulls the names of all
> the databases so I was wondering if anything has changed it worked two
> years ago

I'm struggling to identify where the code might do anything to find 

As far as I can see, the code you sent does the following:
- loads the registry from our public MySQL server for Ensembl Genomes 
(all dbs, not just dicty - the use of -verbose prints out all the 
species it finds, which may be what you're seeing in your output)
- creates a connection to a local MySQL db called 'x' and creates a 
SqlHelper object using that connection
- uses the connection (not the helper) to create an table called introns 
but then does nothing more

Can you shed any more light on the code you'd use to find the introns?



Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/

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