[ensembl-dev] [ensemblgenomes] exception when using list_stable_ids() with Borrelia recurrentis

[Andreas Kusalananda Kähäri]

Hi Giuseppe,

Thanks for finding this. It seems as if the list_stable_ids() method
in the GeneAdaptor is horribly broken, and has been broken since I
made a change to the BaseAdaptor code in June 2010 to support
multi-species core databases. Amazing that nobody else has reported
it!

I (or someone) will look at this and fix it over the week, hopefully tomorrow.

Kind regards,
Andreas K.



On 10 August 2011 19:11, Giuseppe G. <G.Gallone at sms.ed.ac.uk> wrote:
> Hi,
>
> I was trying to retrieve the gene list for Borrelia recurrentis and stumbled
> upon the following exception after doing
>
> my $gene_adaptor = $registry->get_adaptor('Borrelia
> recurrentis','core','Gene');
> my @genes = @{$gene_adaptor->list_stable_ids()};
>
>
> DBD::mysql::st execute failed: Unknown column 'seq_region_id' in 'from
> clause' at
> /home/giuseppe/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line
> 299.
>
> -------------------- EXCEPTION --------------------
> MSG: Detected an error whilst executing SQL 'SELECT stable_id FROM
> gene_stable_id
> JOIN seq_region USING (seq_region_id)
> JOIN coord_system cs USING (coord_system_id)
> WHERE cs.species_id = ?
> ': DBD::mysql::st execute failed: Unknown column 'seq_region_id' in 'from
> clause' at /ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line 299.
>
> STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::_list_dbIDs
> ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:300
> STACK Bio::EnsEMBL::DBSQL::GeneAdaptor::list_stable_ids
> /ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm:172
> Ensembl API version = 63
> ---------------------------------------------------
>
>
> Your help is as usual greatly appreciated.
>
> Best,
> G
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-- 
Andreas Kusalananda Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom