[ensembl-dev] variation allele population name

[Will McLaren]

Hello,

You can get all the populations via a population adaptor:

my $pa = Bio::EnsEMBL::Registry->get_adaptor("human", "variation",
"population");
my @all_populations = @{$pa->fetch_all()};

This will give you a very long list however, as we import all
populations from dbSNP and also have additional populations
representing tissue types from the COSMIC somatic mutation database.

Release 60 of Ensembl (due next week) will include two additional
methods that you may find interesting:

$pa->fetch_all_1KG_Populations
$pa->fetch_all_HapMap_Populations

(1KG = 1000 genomes)

Cheers,

Will McLaren
Ensembl Variation

On 4 November 2010 14:50,  <mailsvl at fastmail.fm> wrote:
> Hi all,
>
> If you created a variation-feature object, you can do:
>
> my @alleles = @{$vf->variation->get_all_Alleles};
> $population = $alleles[0]->population->name;
>
> To get the population name of the first allele. How can I retrieve all
> possible population names now present in ensembl DB?
>
> Thanks,
> -Stef
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