Nothing
# test <- read.csv("tests/testthat/data_tofilter_bold.csv")
test_that("Test refdb_filter_seq_length", {
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
test$nucleotides[1] <- bioseq::dna("ACGT")
res <- refdb_filter_seq_length(test, min_len = 5)
expect_equal(nrow(res), nrow(test) - 1)
test$nucleotides[1] <- bioseq::dna(paste(rep("ACGT", 10000), collapse = ""))
res <- refdb_filter_seq_length(test, max_len = 1000)
expect_equal(nrow(res), nrow(test) - 1)
test$nucleotides[1] <- bioseq::dna("ACGT")
test$nucleotides[2] <- bioseq::dna(paste(rep("ACGT", 10000), collapse = ""))
res <- refdb_filter_seq_length(test, min_len = 5, max_len = 1000)
expect_equal(nrow(res), nrow(test) - 2)
})
test_that("Test refdb_filter_seq_ambiguous", {
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
test$nucleotides[1] <- bioseq::dna("ACGTACNNGTACGT")
res <- refdb_filter_seq_ambiguous(test, max_ambig = 3)
expect_equal(nrow(res), nrow(test))
test$nucleotides[1] <- bioseq::dna("ACGTACNNNNGTACGT")
res <- refdb_filter_seq_ambiguous(test, max_ambig = 3)
expect_equal(nrow(res), nrow(test) - 1)
test$nucleotides[1] <- bioseq::dna("ACGTACNNGTACRRRGT")
res <- refdb_filter_seq_ambiguous(test, max_ambig = 3, char = c("N", "R"))
expect_equal(nrow(res), nrow(test) - 1)
})
test_that("Test refdb_filter_seq_homopolymers", {
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
test$nucleotides[1] <- bioseq::dna("ACGTACAAAAAAAAAAAAAAAAGTACGT")
res <- refdb_filter_seq_homopolymers(test, max_len = 14)
expect_equal(nrow(res), nrow(test) - 1)
test$nucleotides[1] <- bioseq::dna("ACGTACAAAAAAAAAAAAAAAAGTACGT")
res <- refdb_filter_seq_homopolymers(test, max_len = 20)
expect_equal(nrow(res), nrow(test))
})
test_that("Test refdb_filter_seq_duplicates", {
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
test[2, ] <- test[10, ]
res <- refdb_filter_seq_duplicates(test)
expect_equal(nrow(res), nrow(test) - 1)
})
test_that("Test refdb_filter_seq_stopcodon", {
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
test$nucleotides[1] <- bioseq::dna("AAA")
res <- refdb_filter_seq_stopcodon(test, code = 5, codon_frame = 1)
expect_equal(nrow(res), 1)
test$nucleotides[1] <- bioseq::dna("AAA")
res <- refdb_filter_seq_stopcodon(test, code = 5, codon_frame = NA)
expect_equal(nrow(res), nrow(test))
})
test_that("Test refdb_filter_seq_primer", {
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
res <- refdb_filter_seq_primer(test,
primer_forward = NULL,
primer_reverse = NULL)
expect_equal(nrow(res), nrow(test))
test$nucleotides[1] <- bioseq::dna("ACGTAAAAAAACGTAACGTGGGGGGGGTA")
test$nucleotides[10] <- bioseq::dna("ACGTAAAAAAACGTA")
res <- refdb_filter_seq_primer(test,
primer_forward = "AAAAAAA",
primer_reverse = "GGGGGGGG")
expect_equal(nrow(res), 1)
res <- refdb_filter_seq_primer(test,
primer_reverse = "GGGGGGGG")
expect_equal(nrow(res), 1)
res <- refdb_filter_seq_primer(test,
primer_forward = "TTTTTTTTTTT")
expect_equal(nrow(res), 0)
})
test_that("Test refdb_filter_tax_precision", {
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
res <- refdb_filter_tax_precision(test, min_tax = "species_name")
expect_equal(nrow(res), nrow(test))
res <- refdb_filter_tax_precision(test, min_tax = "genus_name")
expect_equal(nrow(res), nrow(test))
test$species_name[3] <- NA
res <- refdb_filter_tax_precision(test, min_tax = "species_name")
expect_equal(nrow(res), nrow(test) - 1)
test$species_name[3] <- "Cloeon dipterum"
test$genus_name[3] <- NA
res <- refdb_filter_tax_precision(test, min_tax = "species_name")
expect_equal(nrow(res), nrow(test))
})
test_that("Test refdb_filter_ref_scope", {
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
test$refs <- rep("REF_1", nrow(test))
test <- refdb_set_fields(test, reference = "refs")
res <- refdb_filter_ref_scope(test, max_tax = "genus_name")
expect_equal(nrow(res), 0)
res <- refdb_filter_ref_scope(test, max_tax = "family_name")
expect_equal(nrow(res), nrow(test))
test$class_name[3] <- "Anotherclass"
test[3, attributes(test)$refdb_fields$taxonomy] <-
rep("Another", length(attributes(test)$refdb_fields$taxonomy))
res <- refdb_filter_ref_scope(test, max_tax = "family_name")
expect_equal(nrow(res), 0)
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
test$refs <- rep("REF_1", nrow(test))
test$refs[1:10] <- rep("REF_2", 10)
test <- refdb_set_fields(test, reference = "refs")
res <- refdb_filter_ref_scope(test, max_tax = "genus_name")
expect_equal(nrow(res), nrow(test) - 10)
})
test_that("Test refdb_filter_tax_na", {
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
test[3, c("genus_name", "species_name")] <- NA
res <- refdb_filter_tax_na(test)
expect_equal(nrow(res), nrow(test) - 1)
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
test[5, c("genus_name", "species_name")] <- NA
test[5, c("genus_name")] <- "Neogen"
res <- refdb_filter_tax_na(test)
expect_equal(nrow(res), nrow(test))
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
test[7, c("order_name")] <- NA
res <- refdb_filter_tax_na(test)
expect_equal(nrow(res), nrow(test))
test <- read.csv("data_tofilter_bold.csv")
test <- refdb_set_fields_BOLD(test)
test[1:2, c("species_name")] <- NA
res <- refdb_filter_tax_na(test)
expect_equal(nrow(res), nrow(test))
})
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