How To Ignore Species In Ensembl Biomart
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Entering edit mode
7.3 years ago
pld 4.9k

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.

perl ensembl biomart • 1.6k views
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2
Entering edit mode

You seem to have the species specified in your code:

$query->setDataset("hsapiens_gene_ensembl");

Is it doing something you don't expect?

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0
Entering edit mode

Any time I've used Ensembl, step two is "choose species", so I don't understand what you mean by "it is gathering all species that are in ensembl." Can you provide more specific details about how you are accessing Ensembl?

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0
Entering edit mode

Thanks for the edit. I generally use R/biomaRt, not the Perl registry, so have not seen this issue. Hopefully our friendly Ensembl outreach have some ideas.

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0
Entering edit mode

Sorry for the cruddy OP, I got distracted and submitted before I finished. Is this possible in biomaRt?

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1
Entering edit mode

In biomaRt, I'd type:

library(biomaRt)
mart.hs <- useMart("ensembl", "hsapiens_gene_ensembl")

and the useMart() function might take a few seconds to run, at most.

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