tests/testthat/test-pkg-Biostrings.R

In tidysq: Tidy Processing and Analysis of Biological Sequences

skip_if_not_installed("Biostrings")

# SETUP ----
str_dna <- c("TACTGGGCATG", "CAGGTCGGA", "TAGTAGTCCG", "", "ACGGT")
str_1_dna <- "TCYYCAHGGCHA"
str_rna <- c("", "KBS-UVW-AWWWG", "YGHHH-", "-CRASH", "MND-KUUBV-MY-")
str_1_rna <- "UUACGACGGCGCAU"
str_ami <- c("OUTLANDISH", "UNSTRUCTURIZED", "FEAR")
str_1_ami <- "PASVKNFYD"
str_unt <- c("vip01", "vip02", "vip04", "missing_one")
str_1_unt <- "2high4U"

sq_dna <- sq(str_dna, alphabet = "dna_bsc")
sq_dna_ext <- sq(str_dna, alphabet = "dna_ext")
sq_1_dna <- sq(str_1_dna, alphabet = "dna_ext")
sq_rna <- sq(str_rna, alphabet = "rna_ext")
sq_1_rna <- sq(str_1_rna, alphabet = "rna_bsc")
sq_1_rna_ext <- sq(str_1_rna, alphabet = "rna_ext")
sq_ami <- sq(str_ami, alphabet = "ami_ext")
sq_1_ami <- sq(str_1_ami, alphabet = "ami_bsc")
sq_1_ami_ext <- sq(str_1_ami, alphabet = "ami_ext")
sq_unt <- sq(str_unt, alphabet = "unt")
sq_1_unt <- sq(str_1_unt, alphabet = "unt")

# Names below are just chosen for extravagance, not political reasons
names_dna <- c("balalaika", "perestroyka", "sojuz", "oncePutin", "LenOut")
names_rna <- c("Monza", "Imola", "Mugello", "Pescara", "Modena")
names_ami <- c("naiz", "haiz", "da")
names_unt <- c("gara", "zara", "zarete", "dira")

biostr_dna <- Biostrings::DNAStringSet(str_dna)
biostr_dna_list <- Biostrings::DNAStringSetList(biostr_dna, biostr_dna)
biostr_dna_n <- Biostrings::DNAStringSet(setNames(str_dna, names_dna))
biostr_1_dna <- Biostrings::DNAString(str_1_dna)
biostr_rna <- Biostrings::RNAStringSet(str_rna)
biostr_rna_n <- Biostrings::RNAStringSet(setNames(str_rna, names_rna))
biostr_1_rna <- Biostrings::RNAString(str_1_rna)
biostr_ami <- Biostrings::AAStringSet(str_ami)
biostr_ami_n <- Biostrings::AAStringSet(setNames(str_ami, names_ami))
biostr_1_ami <- Biostrings::AAString(str_1_ami)
biostr_unt <- Biostrings::BStringSet(str_unt)
biostr_unt_n <- Biostrings::BStringSet(setNames(str_unt, names_unt))
biostr_1_unt <- Biostrings::BString(str_1_unt)

expect_exported_biostrings_set_equal <- function(x, y) {
  expect_true(all(x == y))
  expect_equal(x@ranges, y@ranges)
  expect_equal(x@elementType, y@elementType)
  expect_equal(x@elementMetadata, y@elementMetadata)
  expect_equal(x@metadata, y@metadata)
}

expect_exported_biostrings_item_equal <- function(x, y) {
  expect_true(all(x == y))
  expect_equal(x@offset, y@offset)
  expect_equal(x@length, y@length)
  expect_equal(x@elementMetadata, y@elementMetadata)
  expect_equal(x@metadata, y@metadata)
}

# IMPORT ----
test_that("correctly imports Biostrings::DNAStringSet", {
  expect_identical(import_sq(biostr_dna)[["sq"]],
                   sq_dna_ext)
  expect_identical(import_sq(biostr_dna_n)[["sq"]],
                   sq_dna_ext)
  expect_identical(import_sq(biostr_dna_n)[["name"]],
                   names_dna)
})
test_that("correctly imports Biostrings::DNAString", {
  expect_identical(import_sq(biostr_1_dna)[["sq"]],
                   sq_1_dna)
})

test_that("correctly imports Biostrings::RNAStringSet", {
  expect_identical(import_sq(biostr_rna)[["sq"]],
                   sq_rna)
  expect_identical(import_sq(biostr_rna_n)[["sq"]],
                   sq_rna)
  expect_identical(import_sq(biostr_rna_n)[["name"]],
                   names_rna)
})
test_that("correctly imports Biostrings::RNAString", {
  expect_identical(import_sq(biostr_1_rna)[["sq"]],
                   sq_1_rna_ext)
})

test_that("correctly imports Biostrings::AAStringSet", {
  expect_identical(import_sq(biostr_ami)[["sq"]],
                   sq_ami)
  expect_identical(import_sq(biostr_ami_n)[["sq"]],
                   sq_ami)
  expect_identical(import_sq(biostr_ami_n)[["name"]],
                   names_ami)
})
test_that("correctly imports Biostrings::AAString", {
  expect_identical(import_sq(biostr_1_ami)[["sq"]],
                   sq_1_ami_ext)
})

test_that("correctly imports Biostrings::BStringSet", {
  expect_identical(import_sq(biostr_unt)[["sq"]],
                   sq_unt)
  expect_identical(import_sq(biostr_unt_n)[["sq"]],
                   sq_unt)
  expect_identical(import_sq(biostr_unt_n)[["name"]],
                   names_unt)
})
test_that("correctly imports Biostrings::BString", {
  expect_identical(import_sq(biostr_1_unt)[["sq"]],
                   sq_1_unt)
})

test_that("correctly imports Biostrings::XStringSetList", {
  expect_identical(import_sq(biostr_dna_list),
                   list(import_sq(biostr_dna), import_sq(biostr_dna)))
  expect_identical(import_sq(biostr_dna_list, separate = FALSE),
                   dplyr::bind_rows(import_sq(biostr_dna), import_sq(biostr_dna)))
})

# EXPORT ----
test_that("correctly exports sq object to Biostrings::DNAStringSet", {
  expect_exported_biostrings_set_equal(export_sq(sq_dna, "Biostrings::DNAStringSet"),
                                       biostr_dna)
  expect_exported_biostrings_set_equal(export_sq(sq_dna, "Biostrings::DNAStringSet", name = names_dna),
                                       biostr_dna_n)
})
test_that("correctly exports sq object to Biostrings::DNAString", {
  expect_exported_biostrings_item_equal(export_sq(sq_1_dna, "Biostrings::DNAString"),
                                        biostr_1_dna)
})

test_that("correctly exports sq object to Biostrings::RNAStringSet", {
  expect_exported_biostrings_set_equal(export_sq(sq_rna, "Biostrings::RNAStringSet"),
                                       biostr_rna)
  expect_exported_biostrings_set_equal(export_sq(sq_rna, "Biostrings::RNAStringSet", name = names_rna),
                                       biostr_rna_n)
})
test_that("correctly exports sq object to Biostrings::RNAString", {
  expect_exported_biostrings_item_equal(export_sq(sq_1_rna, "Biostrings::RNAString"),
                                        biostr_1_rna)
})

test_that("correctly exports sq object to Biostrings::AAStringSet", {
  expect_exported_biostrings_set_equal(export_sq(sq_ami, "Biostrings::AAStringSet"),
                                       biostr_ami)
  expect_exported_biostrings_set_equal(export_sq(sq_ami, "Biostrings::AAStringSet", name = names_ami),
                                       biostr_ami_n)
})
test_that("correctly exports sq object to Biostrings::AAString", {
  expect_exported_biostrings_item_equal(export_sq(sq_1_ami, "Biostrings::AAString"),
                                        biostr_1_ami)
})

# EDGE CASES ----
test_that("Biostrings::XString without Set demands sq of length 1", {
  expect_error(
    export_sq(sq_dna, "Biostrings::DNAString"),
    regexp = "sq object must contain exactly one sentence.*"
  )
  expect_error(
    export_sq(sq_rna, "Biostrings::RNAString"),
    regexp = "sq object must contain exactly one sentence.*"
  )
  expect_error(
    export_sq(sq_ami, "Biostrings::AAString"),
    regexp = "sq object must contain exactly one sentence.*"
  )
})