[ensembl-dev] Getting import_vcf.pl working
Andy Yates
ayates at ebi.ac.uk
Wed Feb 27 09:45:35 GMT 2013
Hi Alexander,
Whenever you see an error like "Cannot call dbc on an undefined variable" it normally means that a registry lookup was attempted and no database adaptor was found for your species & group combination. Looking at your example registry file I can see a possible issue with how you have defined your aliases. The value you give as the first parameter to add_alias *must* match the name of the species in the DBAdaptor. I would change your code to:
Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
-species => 'Homo_sapiens',
-alias => ['Homo sapiens', 'H_Sapiens', 'human']
);
You can see the -species parameter now matches the values given to the DBAdaptor.
Hope this helps,
Andy
Andrew Yates Ensembl Core Software Project Leader
EMBL-EBI Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK http://www.ensembl.org/
On 27 Feb 2013, at 00:38, "Tchourbanov, Alexander Y - (atchourb)" <atchourb at email.arizona.edu> wrote:
> Dear ENSEMBL developers,
>
> I have modified the registry in a way it was suggested as listed below:
>
> use strict;
>
> use Bio::EnsEMBL::Utils::ConfigRegistry;
> use Bio::EnsEMBL::DBSQL::DBAdaptor;
> use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
> use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
>
> new Bio::EnsEMBL::DBSQL::DBAdaptor(
> -species => 'Homo_sapiens',
> -user => 'atchourb',
> -pass => 'abcd1234',
> -host => 'localhost',
> -port => '3306',
> -dbname => 'homo_sapiens_core_70_37'
> );
>
> new Bio::EnsEMBL::Variation::DBSQL::DBAdaptor(
> -species => 'Homo_sapiens',
> -user => 'atchourb',
> -pass => 'abcd1234',
> -host => 'localhost',
> -port => '3306',
> -dbname => 'VCFdump'
> );
>
> my @aliases = ( 'H_Sapiens', 'human' );
>
> Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
> -species => 'Homo sapiens',
> -alias => \@aliases
> );
>
> 1;
>
> Now I am getting the following error:
>
> Can't call method "dbc" without a package or object reference at /data/Alex/EnsemblAPI/ensembl-variation/scripts/import/import_vcf.pl line 1268.
> and the application lists all the command line parameters. What do I need to change further for this simple case to work, I want to populate the database VCFdump with the variants that we have here, and all the database connectivity to the best of my knowledge should work without problems, I have been able to connect to the database with JDBC connection. Is there simple way to debug this situation to see what is missing in "dbc" object?
>
> Thanks for all the suggestions,
>
> Alexander
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