tests/testthat/test_data.R

In ucl-pathgenomics/cmvdrg: Human CMV Drug Resistance Genotyping

context("calling resistance")

library(cmvdrg)


test_that("variant files return resistance", {
  expect_equal(nrow(call_resistance(infile = system.file("testdata",  "A10.vcf", package = "cmvdrg"), 
                                    all_mutations = FALSE, inc_anecdotal = F)), 9)
  expect_equal(nrow(call_resistance(infile = system.file("testdata",  "A10.vcf", package = "cmvdrg"), 
                                    all_mutations = FALSE, inc_anecdotal = T)), 11)
  expect_equal(nrow(call_resistance(infile = system.file("testdata",  "A10.vcf", package = "cmvdrg"),all_mutations = T)), 1980)
  expect_equal(nrow(call_resistance(infile = system.file("testdata",  "A10.tab", package = "cmvdrg"),
                                    all_mutations = FALSE, inc_anecdotal = T)), 4)
  expect_equal(nrow(call_resistance(infile = system.file("testdata",  "snpsites.vcf", package = "cmvdrg"),
                                    all_mutations = FALSE, inc_anecdotal = T)), 2)
})

# travis seems a real faff to get working for snp-sites 2.3 as it's r builds are xenial not bionic ubuntu. so ignoring fasta tests for now.
# tested regularly locally. mafft and snp-sites don't need to be tested alone.