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

[Stefano Giorgetti]

... better with Jon being among addressees

S

On 13/02/2023 16:02, Stefano Giorgetti wrote:
>
> 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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>
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-- 
—
Stefano Giorgetti
Ensembl Infrastructure Team Leader, EMBL-EBI
sgiorgetti at ebi.ac.uk
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