[ensembl-dev] import_vcf.pl - ERROR: Could not get population adaptor

Will McLaren wm2 at ebi.ac.uk
Wed Mar 6 09:29:16 GMT 2013


Hi Phil,

The adaptor you create in your registry needs to be under the Variation
sub-class:

new Bio::EnsEMBL::Variation::DBSQL::DBAdaptor(

instead of

new Bio::EnsEMBL::DBSQL::DBAdaptor(

Regards

Will McLaren
Ensembl Variation


On 5 March 2013 20:59, Phil Dagosto <PDagosto at edgebio.com> wrote:

>  I'm trying to import a VCF file into my local Ensembl variation database.
> ****
>
> ** **
>
> The version of the API I'm using is 70.****
>
> ** **
>
> Here are the contents of  my registry file:****
>
> ** **
>
> use Bio::EnsEMBL::Utils::ConfigRegistry;****
>
> use Bio::EnsEMBL::DBSQL::DBAdaptor;****
>
> use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;****
>
> ** **
>
> new Bio::EnsEMBL::DBSQL::DBAdaptor(****
>
>   -host    => 'local_ensembl',****
>
>   -user    => 'test',****
>
>   -pass    => '123',                                   ** **
>
>   -port    => '3306',****
>
>   -species => 'Homo sapiens',****
>
>   -group   => 'variation',****
>
>   -dbname  => 'homo_sapiens_variation_70_37'****
>
> );****
>
> ** **
>
> my @aliases = ( 'H_Sapiens', 'human' );****
>
> ** **
>
> Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(****
>
>   -species => 'Homo sapiens',****
>
>   -alias   => \@aliases****
>
> );****
>
> ** **
>
> 1;****
>
> ** **
>
> The import_vcf .pl script is being run with the following command-line
> parameters:****
>
> ** **
>
> --input_file indel.final.vcf --registry registry.pl --source 'edgebio'
> --population 'test' --test 100****
>
> ** **
>
> The output is:****
>
> ** **
>
> 2013-03-05 15:54:33 - Session ID is 64494fac5e75b495bfb5907137f45cbf****
>
> 2013-03-05 15:54:40 - Connected to database homo_sapiens_variation_70_37
> on local_ensembl as user test****
>
> ERROR: Could not get population adaptor****
>
> ** **
>
> Is there something I need to add to my Registry file so that the
> population adaptor can be found?****
>
> ** **
>
> Thanks,****
>
> ** **
>
> Phil****
>
> ** **
>
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