tests/testthat/test_external_tools.R

In annovarR: Integrated Framework to Annotate Genetic Variants

test_that("annovar", {
  down.dbname <- "refGene"
  x <- annovar("perl", down.dbname = "avsnp147", annovar.dir = "~/tmp/annovar.dir", 
    debug = TRUE)
  expect_that(is.character(x), equals(TRUE))
  x <- annovar("perl", cmd.used = "script1.gene.based", annovar.dir = "~/tmp/annovar.dir", 
    debug = TRUE)
  expect_that(is.character(x), equals(TRUE))
  x <- annovar("perl", cmd.used = "script1.region.based", anno.names = "cytoBand", 
    annovar.dir = "~/tmp/annovar.dir", debug = TRUE)
  expect_that(is.character(x), equals(TRUE))
  x <- annovar("perl", cmd.used = "script1.filter.based", anno.names = "avsnp147", 
    annovar.dir = "~/tmp/annovar.dir", debug = TRUE)
  expect_that(is.character(x), equals(TRUE))
  x <- annovar("perl", cmd.used = "script2", anno.names = c("refGene", "cytoBand", 
    "avsnp147"), input.file = "example.avinput", annovar.dir = "~/tmp/annovar.dir", 
    debug = TRUE)
  expect_that(is.character(x), equals(TRUE))
  x <- annovar("perl", cmd.used = "script3", format = "vcf4old", input.file = "example.vcf", 
    convert.out = "example.avinput", annovar.dir = "~/tmp/annovar.dir", debug = TRUE)
  expect_that(is.character(x), equals(TRUE))
})

test_that("vep", {
  x <- vep(debug = TRUE)
  expect_that(is.character(x), equals(TRUE))
})

test_that("vcfanno", {
  x <- vcfanno(debug = TRUE)
  expect_that(is.character(x), equals(TRUE))
})