run_oc_req: build a runnable python program that posts a file of variants...

In vjcitn/oc2bioc: simple interfaces from OpenCRAVAT to Bioconductor

Description

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

Usage

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_*

vjcitn/oc2bioc documentation built on Aug. 11, 2021, 1:04 p.m.