[ensembl-dev] GO adaptor in latest ensemblgenomes release

[ek]

to use the latest code

  -DBNAME => 'ensemblgenomes_ontology_10_63',

should be

  -DBNAME => 'ensemblgenomes_ontology_21_74',

regards

Eugene

On 2014-02-24 11:57, Simon Andrews wrote:
> The latest ensemblgenomes release (just downloaded from the website -
> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensemblgenomes-21-74&view=tar)
> doesn't allow me to get a GO adapter to use in our scripts.
> 
> #!/usr/bin/perl
> use warnings;
> use strict;
> use lib ("/home/andrewss/EnsemblAPI/bioperl-live");
> use lib ("/home/andrewss/EnsemblAPI/plants/ensembl/modules");
> use Bio::EnsEMBL::Registry;
> use Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
> 
>  warn "Loading Registry information - please be patient\n";
> 
>   my $registry = 'Bio::EnsEMBL::Registry';
> 
>   $registry->load_registry_from_db(
>                                  -host => 'mysql.ebi.ac.uk',
>                                  -port => 4157,
>                                  -user => 'anonymous'
>                                 );
> 
> #  $registry -> set_disconnect_when_inactive(1);
> 
>   my $ontology_dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor -> new (
> 
> -SPECIES => 'Multi',
> 
> -GROUP => 'ontology',
> 
> -HOST => 'mysql.ebi.ac.uk',
> 
> -PORT => 4157,
> 
> -USER => 'anonymous',
> 
> -DBNAME => 'ensemblgenomes_ontology_10_63',
>                                                                    );
> 
> my $GO_adapter =   $registry->get_adaptor( 'Multi', 'Ontology', 
> 'GOTerm' );
> 
> DBD::mysql::st execute failed: Unknown column 'species_id' in 'where
> clause' at
> /home/andrewss/EnsemblAPI/plants/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
> line 139.
> DBD::mysql::st execute failed: Unknown column 'species_id' in 'where
> clause' at
> /home/andrewss/EnsemblAPI/plants/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
> line 139.
> 
> Any ideas?
> 
> Thanks
> 
> Simon.
> 
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