I want to use the BioMart to access ensembl with the registry
ensembl_mart_75, but I'm only interested in a specific list of species. When I run it now, I can see that it is gathering all species that are in ensembl, is it possible to specify which species to choose?
I am accessing Ensembl via the BioMart Perl module.
Suppose I run the following code:
use strict; use BioMart::Initializer; use BioMart::Query; use BioMart::QueryRunner; my $confFile = "conf.reg"; my $action='cached'; my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action); my $registry = $initializer->getRegistry; my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default'); $query->setDataset("hsapiens_gene_ensembl"); $query->addAttribute("ensembl_gene_id"); $query->formatter("TSV"); $query_runner = BioMart::QueryRunner->new; $query_runner->execute($query); $query_runner->printResults;
If the configuration for my registry file has not yet been performed, it attempts to configure for all species in ensembl. This takes a while, I wanted to see if there was a way to speed this up by only configuring for species I want, rather than all of them.