tests/testthat/test-kmr_calc_k_limit.R

In c5sire/kmerize: K-Mer Tools for Building Databases

context("K limit")
testthat::skip_on_appveyor()
testthat::skip_on_travis()
testthat::skip_on_cran()

skip_if_not(kmerize:::get_os() == "Windows", "Skipping image creation on Mac.")

fa <- system.file("testdata/phix174.fasta",
  package = "kmerize"
)
k <- as.integer(seq(5, 17, 2))

tmd <- tempdir()

pr <- file.path(tmd, "test.png")
pr2 <- file.path(tmd, "test_w_k.png")

test_that("kmer counter runs without error", {
  testthat::skip_on_appveyor()
  testthat::skip_on_travis()
  testthat::skip_on_cran()

  res <- kmr_response(fa, k)


  png(pr)
  kmr_plot_response(res)
  dev.off()


  png(pr2)
  kmr_plot_response(res, ref_k = 31)
  dev.off()


  expect_true(
    kmr_calc_k_limit(res)$k == 9
  )
})


context("Plot the genomic response")

test_that("Plot exists", {
  testthat::skip_on_appveyor()
  testthat::skip_on_travis()
  testthat::skip_on_cran()

  expect_true(
    file.exists(pr) == TRUE
  )
})


test_that("Plot has expected size", {
  testthat::skip_on_appveyor()
  testthat::skip_on_travis()
  testthat::skip_on_cran()

  expect_true(
    file.size(pr)[1] >= 300
  )
})



context("Plot the genomic response with ref k")

test_that("Plot exists", {
  testthat::skip_on_appveyor()
  testthat::skip_on_travis()
  testthat::skip_on_cran()

  expect_true(
    file.exists(pr2)
  )
})


test_that("Plot has expected size", {
  testthat::skip_on_appveyor()
  testthat::skip_on_travis()
  testthat::skip_on_cran()

  expect_true(
    file.size(pr2)[1] >= 300
  )
})