tests/testthat/test-print_taxonomy.R

In phylotypr: Classifying DNA Sequences to Taxonomic Groupings

test_that("Print out consesnsus taxonomy", {
  oscillospiraceae <- list(
    taxonomy = c(
      "Bacteria", "Bacillota", "Clostridia",
      "Eubacteriales", "Oscillospiraceae"
    ),
    confidence = c(100, 100, 99, 99, 98)
  )

  expected <- "Bacteria(100);Bacillota(100);Clostridia(99);Eubacteriales(99);Oscillospiraceae(98);Oscillospiraceae_unclassified(98)" # nolint: line_length_linter

  tax_string <- print_taxonomy(oscillospiraceae, n_levels = 6)

  expect_equal(tax_string, expected)


  tax_string <- print_taxonomy(oscillospiraceae)
  expect_equal(tax_string, expected)


  bacteroidales <- list()
  bacteroidales[["taxonomy"]] <- c("Bacteria", "Bacteroidota", "Bacteroidia", "Bacteroidales") # nolint: line_length_linter
  bacteroidales[["confidence"]] <- c(100, 100, 97, 97)
  expected <- "Bacteria(100);Bacteroidota(100);Bacteroidia(97);Bacteroidales(97);Bacteroidales_unclassified(97);Bacteroidales_unclassified(97)" # nolint: line_length_linter

  tax_string <- print_taxonomy(bacteroidales, n_levels = 6)

  expect_equal(tax_string, expected)
})