Variations with Ensembl Regulatory Features

Question

[waqasnayab]

Hi,

Is there any way to get a list of variants that are presentt within ensembl regulatroy feature, that is, get a list of SNPs that are present in any ENSR ID, particulalry in an enhancer ID.

I got some clue from here (http://www.ensembl.info/blog/2013/01/24/variants-in-regulatory-regions-2/ and http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1RegulatoryFeatureVariationAdaptor.html) but not sure is this the right way...,,!!!???

Thanks,

Waqas.

[Emily]

I've let my colleagues in charge of the Ensembl variation API know about your question and they will get back to you.

Answer 1

[Anja_Ensembl]

You can get the data by using Ensembl's API. In the synopsis for the RegulatoryFeatureVariationAdaptor you can find some code examples for how to retrieve variants that overlap regulatory features:

• fetch the RegulatoryFeature object
• use the RegulatoryFeatureVariationAdaptor to fetch all RegulatoryFeatureVariations for the given RegulatoryFeature
• a RegulatoryFeatureVariation object stores information about the RegulatoryFeature and the VariationFeature
• you can retrieve the VariationFeature object by calling variation_feature on the RegulatoryFeatureVariation object: my $variation_feature = $regulatory_feature_variation->variation_feature;
• the VariationFeature object contains information about the variation and location information: http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html

We have more tutorials about how to use our APIs:

• http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html
• http://www.ensembl.org/info/docs/api/funcgen/regulation_tutorial.html
• http://www.ensembl.org/info/docs/api/core/core_tutorial.html

If you already have a checkout of our most recent branch (ensembl-variation(release/84)) could you please pull the most recent changes?

Please let me know if you have more questions.

Answer 2

[waqasnayab]

Hi Anja,

and Thanks, from nothing till here, I am able to perform most of the task.

I am trying to runn this test script available at:

http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1RegulatoryFeatureVariationAdaptor.html

use strict; use warnings; use Bio::EnsEMBL::Registry;

my $reg = 'Bio::EnsEMBL::Registry';

$reg->load_registry_from_db(-host => 'ensembldb.ensembl.org',-user => 'anonymous');

my $rfa  = $reg->get_adaptor('human', 'funcgen', 'RegulatoryFeature');
my $va   = $reg->get_adaptor('human', 'variation', 'Variation');
my $vfa  = $reg->get_adaptor('human', 'variation', 'VariationFeature');
my $rfva = $reg->get_adaptor('human','variation','RegulatoryFeatureVariation');

# fetch RegulatoryFeature by dbID
my $rf_stable_id = 'ENSR00000316845';
my $rf           = $rfa->fetch_by_stable_id($rf_stable_id);

# fetch all RegulatoryFeatureVariations falling in the MotifFeature
my $rfvs = $rfva->fetch_all_by_RegulatoryFeatures([$rf]);

# fetch by VariationFeatures
my $variation_name = 'rs191666497';
my $v   = $va->fetch_by_name($variation_name);
my $vfs = $vfa->fetch_all_by_Variation($v);

# fetch all RegulatoryFeatureVariations for the list of VariationFeatures
for my $vf (@$vfs) {
    print $vf->variation_name, "\n";
}
$rfvs = $rfva->fetch_all_by_VariationFeatures($vfs);
for my $rfv (@$rfvs) {
    print $rfv->regulatory_feature_stable_id, "\n";
}

But I go the following error:

Can't call method "stable_id" on an undefined value at /home/regmwkh/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureOverlapAdaptor.pm line 126.

Do I need to download some thing?

Best,

Waqas.

[Emily]

Please do not post identical questions to BioStars and Ensembl helpdesk. As you've already seen here, Ensembl do monitor BioStars, and posting to both just creates duplicate work.