tests/testthat/test_clean.R

In refdb: A DNA Reference Library Manager

#    test <- read.csv("tests/testthat/data_toclean_bold.csv")

test_that("Test refdb_clean_seq_remove_gaps", {

  test <- read.csv("data_toclean_bold.csv")
  test <- refdb_set_fields_BOLD(test)

  expect_equal(test$nucleotides[1], bioseq::dna("TAC---------TTT----TT"))
  res <- refdb_clean_seq_remove_gaps(test)
  expect_equal(res$nucleotides[1], bioseq::dna("TACTTTTT"))

})



test_that("Test refdb_clean_seq_remove_sideN", {

  test <- read.csv("data_toclean_bold.csv")
  test <- refdb_set_fields_BOLD(test)

  expect_equal(test$nucleotides[2], bioseq::dna("NNNNNNTACTTANNNNNN"))
  res <- refdb_clean_seq_remove_sideN(test, side = "left")
  expect_equal(res$nucleotides[2], bioseq::dna("TACTTANNNNNN"))
  res <- refdb_clean_seq_remove_sideN(test, side = "right")
  expect_equal(res$nucleotides[2], bioseq::dna("NNNNNNTACTTA"))
  res <- refdb_clean_seq_remove_sideN(test, side = "both")
  expect_equal(res$nucleotides[2], bioseq::dna("TACTTA"))

})



test_that("Test refdb_clean_seq_crop_primers", {

  test <- read.csv("data_toclean_bold.csv")
  test <- refdb_set_fields_BOLD(test)

  expect_equal(test$nucleotides[3], bioseq::dna("TGGTCGGCACTTCACTTAGTCTTTTTCTTATACCA"))
  res <- refdb_clean_seq_crop_primers(test,
                                      primer_forward = "GGCACT",
                                      primer_reverse = "TTTTT",
                                      max_error_in = 0,
                                      max_error_out = 0,
                                      include_primers = TRUE)
  expect_equal(res$nucleotides[3], bioseq::dna("GGCACTTCACTTAGTCTTTTT"))

})


test_that("Test refdb_clean_tax_remove_blank", {

  test <- read.csv("data_toclean_bold.csv")
  test <- refdb_set_fields_BOLD(test)

  expect_equal(test$subfamily_name[2], "Baetinae ")
  expect_equal(test$species_name[3], "Baetis  alpinus")
  res <- refdb_clean_tax_remove_blank(test)
  expect_equal(res$subfamily_name[2], "Baetinae")
  expect_equal(res$species_name[3], "Baetis alpinus")

})


test_that("Test refdb_clean_tax_remove_extra", {

  test <- read.csv("data_toclean_bold.csv")
  test <- refdb_set_fields_BOLD(test)

  test$species_name[1] <- "Cloeon dipterum ag415"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Cloeon dipterum")

  test$species_name[1] <- "Cloeon dipterum CBG"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Cloeon dipterum")

  test$species_name[1] <- "Cloeon dipterum X"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Cloeon dipterum")

  test$species_name[1] <- "Cloeon dipterum x"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Cloeon dipterum")

  test$species_name[1] <- "Cloeon dipterum (species)"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Cloeon dipterum")

  test$species_name[1] <- "Cloeon (gen) dipterum"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Cloeon dipterum")

  test$species_name[1] <- "Lutjanus aff. johnii CIFEFGB"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Lutjanus aff. johnii")

  test$species_name[1] <- "Cochliopodium sp. ATCC 30936"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Cochliopodium sp.")

  test$species_name[1] <- "Cortinarius cf. violaceus TRTC155606"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Cortinarius cf. violaceus")

  test$species_name[1] <- "Pristimantis sp. ca MRC"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Pristimantis sp.")

  test$species_name[1] <- "Pristimantis sp. nov. teofanensis MRC"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Pristimantis sp. nov. teofanensis")

  test$species_name[1] <- "Pristimantis teofanensis sp. nov. bg MRC"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Pristimantis teofanensis sp. nov.")

  # Expected no change:
  test$species_name[1] <- "Cloeon dipterum"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Cloeon dipterum")

  test$species_name[1] <- "Saccharomyces cerevisiae * Saccharomyces paradoxus"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], "Saccharomyces cerevisiae * Saccharomyces paradoxus")

  # Expected NA
  test$species_name[1] <- ""
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], as.character(NA))

  test$species_name[1] <- "AGG XXP"
  res <- refdb_clean_tax_remove_extra(test)
  expect_equal(res$species_name[1], as.character(NA))
})



test_that("Test refdb_clean_tax_harmonize_nomenclature", {

  test <- read.csv("data_toclean_bold.csv")
  test <- refdb_set_fields_BOLD(test)

  test$species_name[1] <- "Cloeon species"
  res <- refdb_clean_tax_harmonize_nomenclature(test)
  expect_equal(res$species_name[1], "Cloeon sp.")

  test$genus_name[1] <- "Baetidae familia"
  res <- refdb_clean_tax_harmonize_nomenclature(test)
  expect_equal(res$genus_name[1], "Baetidae fam.")

  test$species_name[1] <- "Cloeon confer dipterum"
  res <- refdb_clean_tax_harmonize_nomenclature(test)
  expect_equal(res$species_name[1], "Cloeon cf. dipterum")

  test$species_name[1] <- "Saccharomyces cerevisiae x Saccharomyces paradoxus"
  res <- refdb_clean_tax_harmonize_nomenclature(test)
  expect_equal(res$species_name[1], "Saccharomyces cerevisiae * Saccharomyces paradoxus")

})



test_that("Test refdb_clean_tax_remove_uncertainty", {

  test <- read.csv("data_toclean_bold.csv")
  test <- refdb_set_fields_BOLD(test)

  test$species_name[1] <- "Cloeon cf. dipterum"
  res <- refdb_clean_tax_remove_uncertainty(test)
  expect_equal(res$species_name[1], "Cloeon dipterum")

  test$species_name[1] <- "Cloeon aff. dipterum"
  res <- refdb_clean_tax_remove_uncertainty(test)
  expect_equal(res$species_name[1], "Cloeon dipterum")

  test$species_name[1] <- "Cloeon sp. inc. dipterum"
  res <- refdb_clean_tax_remove_uncertainty(test)
  expect_equal(res$species_name[1], "Cloeon dipterum")

})


test_that("Test refdb_clean_tax_remove_subsp", {

  test <- read.csv("data_toclean_bold.csv")
  test <- refdb_set_fields_BOLD(test)

  test$species_name[1] <- "Cloeon dipterum var. dipterum"
  res <- refdb_clean_tax_remove_subsp(test)
  expect_equal(res$species_name[1], "Cloeon dipterum")

})



test_that("Test refdb_clean_tax_NA", {

  test <- read.csv("data_toclean_bold.csv")
  test <- refdb_set_fields_BOLD(test)

  test$species_name[1] <- ""
  res <- refdb_clean_tax_NA(test)
  expect_equal(res$species_name[1], as.character(NA))

  test$species_name[1] <- "Lila biluna"
  res <- refdb_clean_tax_NA(test)
  expect_equal(res$species_name[1], "Lila biluna")

  test$species_name[1] <- "Lila sp."
  res <- refdb_clean_tax_NA(test)
  expect_equal(res$species_name[1], as.character(NA))

  test$species_name[1] <- "Lila * Lola"
  res <- refdb_clean_tax_NA(test, hybrid = TRUE)
  expect_equal(res$species_name[1], as.character(NA))

  test$species_name[1] <- "Lila lala * Lola lili"
  res <- refdb_clean_tax_NA(test, hybrid = FALSE)
  expect_equal(res$species_name[1], "Lila lala * Lola lili")

  test$species_name[1] <- "Lila cf. biluna"
  res <- refdb_clean_tax_NA(test, uncertain = TRUE)
  expect_equal(res$species_name[1], as.character(NA))

  test$species_name[1] <- "Lila cf. biluna"
  res <- refdb_clean_tax_NA(test, uncertain = FALSE)
  expect_equal(res$species_name[1], "Lila cf. biluna")

})