[ensembl-dev] question variation APi

Will McLaren wm2 at ebi.ac.uk
Tue Oct 7 13:52:20 BST 2014

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:

| 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,

To answer your question, to fetch somatic mutations use fetch_all_somatic()


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";
>                         }
>                 }
> }
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20141007/e96a6039/attachment.html>

More information about the Dev mailing list