[ensembl-dev] question variation APi
Nathalie Conte
nconte at ebi.ac.uk
Tue Oct 7 10:38:40 BST 2014
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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