tests/testthat/test-label_mutations.R

In bailey-lab/miplicorn: A Framework for Molecular Inversion Probe and Amplicon Analysis

data <- new_ref_alt_cov_tbl(tibble::tribble(
  ~sample, ~ref, ~alt, ~ref_umi_count, ~alt_umi_count, ~coverage,
  "S1", "A", "G", 54, 10, 64,
  "S2", "G", "A", 15, 0, 15,
  "S3", "T", "C", 0, 15, 15,
  "S4", "GA", "G", 2, 18, 20,
  "S5", "G", "ATC", 0, 10, 10
))

res <- new_ref_alt_cov_tbl(tibble::tribble(
  ~sample, ~ref, ~alt, ~ref_umi_count, ~alt_umi_count, ~coverage, ~mutation_label,
  "S1", "A", "G", 54, 10, 64, "ref",
  "S2", "G", "A", 15, 0, 15, "ref",
  "S3", "T", "C", 0, 15, 15, "alt",
  "S4", "GA", "G", 2, 18, 20, "del",
  "S5", "G", "ATC", 0, 10, 10, "ins"
))

test_that("label mutations needs a ref alt cov table", {
  expect_error(label_mutations(tibble::tibble(a = 1)))
  expect_snapshot_error(label_mutations(tibble::tibble(a = 1)))
})

test_that("call columns must exist", {
  expect_error(label_mutations(new_ref_alt_cov_tbl(tibble::tibble(a = 3))))
  expect_error(label_mutations(new_ref_alt_cov_tbl(tibble::tibble(ref = 3))))
  expect_error(label_mutations(new_ref_alt_cov_tbl(tibble::tibble(alt = 3))))
  expect_snapshot_error(
    label_mutations(new_ref_alt_cov_tbl(tibble::tibble(a = 3)))
  )
})

test_that("labels mutations correctly", {
  expect_equal(label_mutations(data), res)
})

test_that("can control position", {
  expect_equal(
    label_mutations(data, .before = ref),
    dplyr::relocate(res, mutation_label, .before = ref)
  )
  expect_equal(
    label_mutations(data, .after = sample),
    dplyr::relocate(res, mutation_label, .after = sample)
  )
})

test_that("error if control position with both .before and .after", {
  expect_error(label_mutations(data, .before = ref, .after = sample))
  expect_snapshot_error(label_mutations(data, .before = ref, .after = sample))
})