tests/testthat/test-tally_tmhs.R

In richelbilderbeek/pureseqtmr: Predict Transmembrane Protein Topology

test_that("one protein with two TMHs", {
  if (!is_pureseqtm_installed()) return()

  topology <- predict_topology(
    get_example_filename("1bhaA.fasta")
  )
  tally <- tally_tmhs(topology)
  expect_true("name" %in% names(tally))
  expect_true("n_tmhs" %in% names(tally))
  expect_equal(nrow(topology), nrow(tally))
  expect_equal(1, nrow(tally))
  expect_equal(2, tally$n_tmhs[1])
})

test_that("one protein with two TMHs, one at the start", {
  if (!is_pureseqtm_installed()) return()

  topology <- predict_topology(
    get_example_filename("1bhaA.fasta")
  )
  topology$topology[1] <- "111111111111100000011111111"
  tally <- tally_tmhs(topology)
  expect_true("name" %in% names(tally))
  expect_true("n_tmhs" %in% names(tally))
  expect_equal(nrow(topology), nrow(tally))
  expect_equal(1, nrow(tally))
  expect_equal(2, tally$n_tmhs[1])
})

test_that("three non-TMHs", {
  if (!is_pureseqtm_installed()) return()

  topology <- predict_topology(
    get_example_filename("test_proteome.fasta")
  )
  tally <- tally_tmhs(topology)
  expect_true("name" %in% names(tally))
  expect_true("n_tmhs" %in% names(tally))
  expect_equal(nrow(topology), nrow(tally))
})