tests/testthat/test-selection.R

In santiago1234/iCodon: iCodon: Designing "ideal" coding (iCodon) sequences for customized expression level

test_that("selection", {
  # initialize optimization function
  sampling_function <- sample_synonimous_codon(sampling_codon_distribution = sampling_optimization)
  evolutor <- evolution(test_seq, sampling_function)
  stability_predictor <- predict_stability("human")
  selector <- selection(stability_predictor, optimization = T)

  # test that picks the fittest sequence
  daughters_1 <- evolutor(test_seq)
  # the seed is just because the random function but needs to be romoved from here

  fitness <- stability_predictor(daughters_1)
  fitest_seq <- daughters_1[which(fitness == max(fitness))]

  expect_equal(selector(daughters_1, 1)$synonymous_seq, fitest_seq)

  # test the same for deoptimization
  selector <- selection(stability_predictor, optimization = F)

  # test that picks the fittest sequence
  daughters_1 <- evolutor(fitest_seq)
  # the seed is just because the random function but needs to be romoved from here
  fitness <- stability_predictor(daughters_1)
  fitest_seq <- daughters_1[which(fitness == min(fitness))]

  expect_equal(selector(daughters_1, 1)$synonymous_seq, fitest_seq)
})