Question: Genome Nexus : API access through R
0
gravatar for Nicolas Rosewick
8 months ago by
Belgium, Brussels
Nicolas Rosewick9.2k wrote:

Hi,

I'm trying to access Genome Nexus API to annotate some variants.

I'm using the example on their github :

https://github.com/genome-nexus/genome-nexus/blob/master/notebooks/genome_nexus_r_example.ipynb

For instance I want to check variant 7:g.55249071C>T (hg19)

On Genome Nexus website everything's ok : https://www.genomenexus.org/variant/7:g.55249071C%3ET

In R :

library(rapiclient)
client <- get_api(url = "https://www.genomenexus.org/v2/api-docs")

operations <- get_operations(client)
res <- operations$fetchVariantAnnotationGET(variant="7:g.55249071C>T")

res
Response [http://www.genomenexus.org/annotation/7:g.55249071C>T]
  Date: 2020-03-06 13:24
  Status: 400
  Content-Type: text/html;charset=utf-8
  Size: 800 B

content(res)
{html_document}
<html lang="en">
[1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">\nHTTP Status 400 – Bad Request\n<style type="text/css">h1 {font-family:Tahoma,Arial,sans ...
[2] <body>

HTTP Status 400 – Bad Request

</body>

Did I miss something here ?

Thanks

R api genome nexus • 164 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by Nicolas Rosewick9.2k
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