[ensembl-dev] question variation APi

[Will McLaren]

Hi Nathalie,

We wouldn't recommend using the API to retrieve all of the rsIDs; there are
>60million and the API is not optimised for retrieving the whole dataset in
this way.

Instead I'd recommend you extract the IDs from one of our dump files;
probably VCF or GVF would be the easiest to work with:

curl
ftp://ftp.ensembl.org/pub/release-77/variation/vcf/homo_sapiens/Homo_sapiens.vcf.gz
| zcat | grep -v # | cut -f 3 | head

(remove the head and redirect to a file to get all of them).

The somatic mutations are in a separate file,
ftp://ftp.ensembl.org/pub/release-77/variation/vcf/homo_sapiens/Homo_sapiens_somatic.vcf.gz

To answer your question, to fetch somatic mutations use fetch_all_somatic()
(see
http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1VariationAdaptor.html#a22e69dacdd77542463320a1ef16b151f
)

Regards

Will McLaren
Ensembl Variation

On 7 October 2014 10:38, Nathalie Conte <nconte at ebi.ac.uk> wrote:

> Hi,
> I would like to get all variation ID  (ie rs1822893 )from ensembl, I am
> using the variation API to do so.
> Is it the best way? the fetch_all method seems to get all germline
> variation, is there another method for somatic ones?
>
> my $vf_adaptor = Bio::EnsEMBL::Registry->get_adaptor('human', 'variation',
> 'variationfeature');
> my @vfs = @{$vf_adaptor->fetch_all()};
> foreach my $vf(@vfs){
>                  if ($vf){
>                         my $varID=defined($vf->variation_name) ?
> $vf->variation_name :'No_variation';
>                         if ($varID) {
> print  "$varID\n";
>                         }
>                 }
> }
>
>
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