tests/testthat/test-run_cobalt.R

In richelbilderbeek/cobaltr: Interface Io COBALT

test_that("use", {
  if (!is_cobalt_installed()) return()
  fasta_filename <- system.file("extdata", "example.fasta", package = "cobaltr")
  fasta_text <- run_cobalt(
    fasta_filename = fasta_filename,
    cobalt_options = create_cobalt_options()
  )
  expect_equal(class(fasta_text), "character")
  expect_equal(4, length(fasta_text))
})

test_that("matrices", {
  if (!is_cobalt_installed()) return()

  fasta_filename <- system.file("extdata", "example.fasta", package = "cobaltr")
  run_cobalt(
    fasta_filename = fasta_filename,
    cobalt_options = create_cobalt_options(score_matrix_name = "BLOSUM62")
  )
  expect_error(
    run_cobalt(
      fasta_filename = fasta_filename,
      cobalt_options = create_cobalt_options(score_matrix_name = "PAM30")
    ),
    "Cannot generate Karlin block"
  )
})