build a runnable python program that posts a file of variants to OpenCRAVAT

build a runnable python program that posts a file of variants to OpenCRAVAT

run_oc_req(
  url = "http://0.0.0.0:8080/submit/submit",
  postfile = "/tmp/abc.txt",
  annotators = c("clinvar", "segway_lung"),
  reports = c("text", "vcf"),
  assembly = "hg38",
  note = "test run"
)

Arguments

url

'submit/submit' OpenCRAVAT endpoint url

postfile

path to file with variants in TSV format

annotators

character() vector of annotator names, must be installed in server identified by `url`

reports

character() vector of reporter names, must be available in server identified by `url`

assembly

character(1) hg38 or hg37

note

character(1) arbitrary string

Value

a reticulate python.builtin.dict with component `r` for which `r$json()` will return metadata about run; an attribute `serverurl` is added with the serverurl string, omitting the `submit/submit...`

Note

This is an extremely fragile and cumbersome approach. It would be better to compose using a JSON constructor, and to use httr::POST. But the quoting requirements and the use of open() in the request seem hard for such an approach.

Examples

if (interactive()) run_oc_req()  # then use reticulate run_py_*