tests/testthat/test-save_map_table.R

In richelbilderbeek/plinkr: Interface to PLINK

test_that("use", {
  map_table <- get_test_map_table()
  map_filename <- get_plinkr_tempfilename()
  save_map_table(
    map_table = map_table,
    map_filename = map_filename
  )
  expect_true(file.exists(map_filename))
  file.remove(map_filename)
})

test_that("detailed use, recreate v1.7 test.map file exactly", {
  if (!is_plink_installed(create_plink_v1_7_options())) return()
  plink_map_filename <- get_plink_example_filename(
    example_filename = "test.map",
    create_plink_v1_7_options()
  )
  map_table <- read_plink_map_file(
    map_filename = plink_map_filename
  )
  map_filename <- get_plinkr_tempfilename()
  save_map_table(
    map_table = map_table,
    map_filename = map_filename,
    plink_options = create_plink_v1_7_options()
  )
  map_table_again <- read_plink_map_file(
    map_filename = map_filename
  )
  expect_equal(names(map_table), names(map_table_again))
  expect_equal(nrow(map_table), nrow(map_table_again))
  expect_equal(ncol(map_table), ncol(map_table_again))
  expect_equal(readLines(plink_map_filename), readLines(map_filename))
  file.remove(map_filename)
})

test_that("detailed use, recreate v1.9 test.map file exactly", {
  if (!is_plink_installed(create_plink_v1_9_options())) return()
  plink_map_filename <- get_plink_example_filename(
    example_filename = "toy.map",
    create_plink_v1_9_options()
  )
  map_table <- read_plink_map_file(
    map_filename = plink_map_filename
  )
  map_filename <- get_plinkr_tempfilename()
  save_map_table(
    map_table = map_table,
    map_filename = map_filename,
    plink_options = create_plink_v1_9_options()
  )
  map_table_again <- read_plink_map_file(
    map_filename = map_filename
  )
  expect_equal(names(map_table), names(map_table_again))
  expect_equal(nrow(map_table), nrow(map_table_again))
  expect_equal(ncol(map_table), ncol(map_table_again))
  expect_equal(readLines(map_filename), readLines(plink_map_filename))
  file.remove(map_filename)
})

test_that("sub-sub-sub folder", {
  map_table <- get_test_map_table()
  map_filename <- file.path(
    get_plinkr_tempfilename(),
    "sub", "sub", "sub", "folder", "test.map"
  )
  save_map_table(
    map_table = map_table,
    map_filename = map_filename
  )
  expect_true(file.exists(map_filename))
  file.remove(map_filename)
  unlink(
    dirname(dirname(dirname(dirname(dirname(map_filename))))),
    recursive = TRUE
  )
})

test_that("Give error due to too high chromosome number", {
  set.seed(314)
  assoc_data <- create_demo_assoc_data(
    n_individuals = 2
  )
  assoc_data$data$map_table$CHR <- 123 # nolint PLINK coding style
  expect_error(
    save_map_table(
      map_table = assoc_data$data$map_table,
      map_filename = "irrelevant"
    ),
    "default PLINK can handle a maximum of 95 chromosomes"
  )
})

test_that("write to impossible folder", {
  # Windows has no impossible folders
  if (get_os() == "win") return()

  map_table <- read_plink_map_file(get_plinkr_filename("toy_95.map"))
  map_filename <- "/root/test.map"

  expect_error(
    save_map_table(
      map_table = map_table,
      map_filename = map_filename
    ),
    "Cannot save 'map_table' to path"
  )
})