[ensembl-dev] GO adaptor in latest ensemblgenomes release

[Simon Andrews]

Thanks - I¹d forgotten that was there, I think that was supposed to be a
temporary fix for a previous problem I had.

I¹m now getting a warning that there is a difference between the software
release (75) and database release (74).  I included the URL I used below
which definitely says that it¹s the v74 branch.  Is this a problem?  Could
some new code have been checked into the wrong branch?

Thanks

Simon.

On 24/02/2014 12:02, "ek" <ek at ebi.ac.uk> wrote:

>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&on
>>ly_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/BaseMe
>>taContainer.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/BaseMe
>>taContainer.pm
>> line 139.
>>
>> Any ideas?
>>
>> Thanks
>>
>> Simon.
>>
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