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

[Giuseppe G.]

Hi Andreas,

thanks a lot for solving that. I should probably say the method seemed 
to work fine with a wide variety of other genomes. I cannot say whether 
it was Borrelia r. only or not.

Best,
G

On 11/08/11 10:50, Andreas Kusalananda Kähäri wrote:
> Hi Giuseppe,
>
> The problem is now solved and the code has been committed.  If you
> can't wait for release 64 to come out, you can update the
> BaseAdaptor.pm module (in ensembl/modules/Bio/EnsEMBL/DBSQL) to the
> latest revision (the patch is in revision 1.59 of the file) through
> CVS.
>
> Cheers,
> K/A
>
> 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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>> with registration number SC005336.
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>
>
>

-- 
Giuseppe Gallone
Centre for Integrative Physiology
School of Biomedical Sciences
University of Edinburgh
Hugh Robson Building
George Square
Edinburgh EH8 9XD

G.Gallone at sms.ed.ac.uk
http://www.cip.ed.ac.uk

The University of Edinburgh is a charitable body, registered in 
Scotland, with registration number SC005336.