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

[Williams, Jonathan (RTH) OUH]

Hello Stefano,

Thanks for the speedy reply. Connecting via "ensembldb.ensembl.org", is this still correct?

Will adapt code to restrict to COSMIC - the performance increase will be useful. I don't think it's a region related issue; matching regions before and after January 2023 returned COSV IDs previously and no longer do now, a separate query to look up gene names using the same declared slice still performs quite happily. Very strange!

Jon

Jonathan Williams DClinSci PhD FRCPath
Principal Clinical Scientist (HSS Registered) | NGS Core and Cancer Genetics

From: Dev <dev-bounces at ensembl.org> On Behalf Of Stefano Giorgetti
Sent: 13 February 2023 16:03
To: dev at ensembl.org
Subject: Re: [ensembl-dev] Changes to COSMIC data storage in ensembl API?


Hello Jon,

The code base hasn't changed significantly transitioning from E!108 to E!109, TBH.

I tried (sort of) your code below, and I could get some IDs back from the API.

Possible differences between our code do not seem enough to explain why you are not retrieving any data:

  *   Used "ensembldb.ensembl.org" host
  *   Focussed on region chr18 between 49481681 and 49492479
  *   returned the first 5 IDs

As additional note, I would check

  1.  you are not connecting to our former US West mirror (which should not be the case)
  2.  you may want to use "$slice->get_all_somatic_VariationFeatures_by_source('COSMIC')" instead of "get_all_somatic_VariationFeatures()"
I am getting 6-fold increase in performance ... if you are interested only in COSMIC variants, of course

Is it maybe region-specific issue?
Feel free to share the regions you are interested in, should you want me to double check.

Hope this helps

Cheers,

Stefano
On 13/02/2023 14:40, Williams, Jonathan (RTH) OUH wrote:
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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