tests/testthat/test-make_BLAST_uuid.R

In andrewrech/antigen.garnish: Tumor neoantigen prediction

testthat::test_that("make_BLAST_uuid", {
  if (length(system("which blastp", intern = TRUE)) != 1) {
    testthat::skip("Skipping antigen.garnish:::make_BLAST_uuid because ncbiblast+ is not in PATH")
  }

  d <- test_data_dir()

  dt <- data.table::fread(file.path(d, "antigen.garnish_test_make_BLAST_uuid.csv"))

  dti <- dt %>%
    data.table::copy() %>%
    .[, MHC := "H-2-Kb"] %>%
    .[, nmer_uuid := uuid::UUIDgenerate(), by = "nmer"] %>%
    .[, sample_id := "my_sample"] %>%
    .[, effect_type := "missense_variant"]

  dto <- antigen.garnish:::make_BLAST_uuid(dti) %>% .[order(nmer)]

  # run test
  testthat::expect_equal(
    dto[!is.na(blast_uuid), nmer],
    c(
      "ENYWRKAY",
      "ENYWRKSY",
      "NYWRKAYE",
      "NYWRKSYE"
    )
  )

  testthat::expect_equal(
    dto[, pep_type],
    c(
      "mutnfs",
      "mutnfs",
      "wt",
      "wt",
      "mutnfs",
      "wt",
      "mutnfs",
      "wt",
      "wt",
      "mutnfs",
      "wt",
      "mutnfs",
      "wt",
      "wt",
      "mutnfs",
      "wt",
      "mutnfs",
      "wt"
    )
  )
})