tests/testthat/test-write_netmhc_nmers.R

In andrewrech/antigen.garnish: Tumor neoantigen prediction

testthat::test_that("write_netmhc_nmers", {
  list.files(pattern = "netMHC.*csv") %>% file.remove()
  on.exit(list.files(pattern = "netMHC_.*csv") %>% file.remove())

  # load test data
  dt <- data.table::data.table(netMHC = c(
    "HLA-A0201", "HLA-A0201", "HLA-A0201",
    "HLA-A0201", "HLA-A0201", "HLA-A0201", "HLA-A0201", "HLA-A0201",
    "HLA-A0201", "HLA-A0201"
  ), nmer = c(
    "AQSGTPPT", "AYESSEDC", "DDENYWRK",
    "ENYWRDDD", "GAQSGTPP", "GTWVSGAQ", "GTWVSGVQ", "GVQSGTPP", "KAYESSED",
    "KSYESSED"
  ), nmer_l = c(8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 8L))

  # run test
  dto <- antigen.garnish:::write_netmhc_nmers(dt, "netMHC")

  testthat::expect_true(
    data.table::fread(dto$filename,
      header = FALSE
    )$V1 %chin%
      c(
        "AQSGTPPT", "AYESSEDC", "DDENYWRK",
        "ENYWRDDD", "GAQSGTPP", "GTWVSGAQ",
        "GTWVSGVQ", "GVQSGTPP", "KAYESSED",
        "KSYESSED"
      ) %>% all()
  )

  testthat::expect_equal(dto$allele %>% unique(), "HLA-A0201")
})