Question: Annotation with Ensembl REST API
0
gravatar for Noushin N
10 days ago by
Noushin N560
Baltimore, MD
Noushin N560 wrote:

I would like to annotate a set of variants in terms of their protein consequence inside a piece of R code. I have tried to model my code after the example from ensembl REST API, but encounter the following error:

Error in curl::curl_fetch_memory(url, handle = handle) :
Could not resolve host: grch37.rest.ensembl.org
Calls: scan_genes ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted

Of note, I submit the variants in batches to avoid time limits (not sure if this is necessary). And this error only happens after about 70 batches of 15 variants have been successfully annotated.

Any insight would be much appreciated!

Best, Noushin

R api ensembl • 62 views
ADD COMMENTlink modified 10 days ago by Emily_Ensembl20k • written 10 days ago by Noushin N560

Tagging: Emily_Ensembl

ADD REPLYlink written 10 days ago by Noushin N560
0
gravatar for Emily_Ensembl
10 days ago by
Emily_Ensembl20k
EMBL-EBI
Emily_Ensembl20k wrote:

I'm afraid we're having problems with our REST server at the moment, particularly grch37.rest.ensembl. We're hoping that something we will do today will fix it, but I can't promise anything. I'm sorry you've had a problem.

ADD COMMENTlink written 10 days ago by Emily_Ensembl20k

Thanks so much for the prompt follow up, Emily_Ensembl . I will try again within a couple of days and see how it looks.

ADD REPLYlink written 10 days ago by Noushin N560
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