Connection timeout when using multiple commands on eutils

Question

[johntikas]

I have successfully constructed a series of functions based on eutils that capture the rsID of a given SNP as a character variable and search for clinical significance strings on clinVAR and dbSNP. When I run every function with apply() on a column of >1000 whole exome sequencing entries I usually get a connection timeout error, unlike running the function for a single variable every time. For example;

> clinVARlookup("rs4340")
[1] "Pathogenic"

> clinVARdisease("rs4340")  
[1] "Microvascular complications of diabetes 3, Ischemic stroke, susceptibility to, Myocardial infarction, ANGIOTENSIN I-CONVERTING ENZYME INSERTION/DELETION POLYMORPHISM, Stroke, hemorrhagic, susceptibility to, Severe acute respiratory syndrome, progression of, Susceptibility to progression to renal failure in IgA nephropathy"

Realistically speaking, what are the alternatives ? I am currently searching for indexing methods based on downloaded databases, but I would prefer not to update >1Gb databases every now and then whenever I want to provide genetic counselling tables.

[Giovanni M Dall'Olio]

Which library are you using? reutils?

[johntikas]

Yes! Any suggestions welcome.

Answer 1

[Newgene]

Try MyVariant.info API:

http://myvariant.info/v1/query?q=rs4340&fields=clinvar

Batch is supported via POST. Also the Python or R clients:

https://pypi.python.org/pypi/myvariant

https://www.bioconductor.org/packages/release/bioc/html/myvariant.html

[Newgene]

also see this related post:

A: Searching for ClinVar entries based on SNP annotation