[ensembl-dev] Changes to COSMIC data storage in ensembl API?

[Williams, Jonathan (RTH) OUH]

Hello All,

As part of a pipeline, I've been using the following code snippet to grab COSMIC variant IDs from specific regions of the human genome - this all worked wonderfully until the beginning of February this year and I'm wondering if the code base has changed with the most recent ensembl release? Any advice on how to do this now, bearing in mind I am definitely a bit of a Bioinformatics amateur?

my $slice_adaptor = $registry->get_adaptor('Human', 'Core', 'Slice');
my $slice = $slice_adaptor->fetch_by_region($coords);
my $vs = $slice->get_all_somatic_VariationFeatures();
my @variants = @{$vs};
foreach (@variants){
                my $name = $_->name();
                push (@variant_list, $name);
};

When this was working the end result was pushing of COSV IDs into the final @variant_list array which I was then able to print against regions in a final report. This array now ends up empty so either the "->name()" parameter or something to do with COSMIC data storage amongst the "get_all_somatic_VariationFeatures" dataset may have been altered...

Jon Williams

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