context("Test: is.genome.available()")
test_that("The is.genome.available() interface to NCBI RefSeq
works properly..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'refseq' works properly
expect_equal(nrow(is.genome.available(db = "refseq",
organism = "Saccharomyces cerevisiae",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "refseq",
organism = "Saccharomyces cerevisiae",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to NCBI RefSeq
works properly using taxid..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'refseq' works properly
expect_equal(nrow(is.genome.available(db = "refseq",
organism = "559292",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "refseq",
organism = "559292",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to NCBI RefSeq
works properly using assembly accession id", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'refseq' works properly
expect_equal(nrow(is.genome.available(db = "refseq",
organism = "GCF_000146045.2",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "refseq",
organism = "GCF_000146045.2",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to NCBI Genbank
works properly..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'genbank' works properly
expect_equal(nrow(is.genome.available(db = "genbank",
organism = "Saccharomyces cerevisiae",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "genbank",
organism = "Saccharomyces cerevisiae",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to NCBI Genbank
works properly using taxid..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'genbank' works properly
expect_equal(nrow(is.genome.available(db = "genbank",
organism = "559292",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "genbank",
organism = "559292",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to NCBI Genbank
works properly using assembly accession id", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'genbank' works properly
expect_equal(nrow(is.genome.available(db = "genbank",
organism = "GCA_000091065.2",
details = TRUE)) > 0, TRUE)
# test whether it works properly a second time based on the internal files
expect_equal(suppressMessages(is.genome.available(db = "genbank",
organism = "GCA_000091065.2",
details = FALSE)), TRUE)
})
test_that("The is.genome.available() interface to Ensembl
works properly..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'ensembl' works properly
expect_equal(nrow(is.genome.available(db = "ensembl",
organism = "Saccharomyces cerevisiae",
details = TRUE)) > 0, TRUE)
# test whether interface to 'ensembl' works properly without details
expect_equal(suppressMessages(is.genome.available(db = "ensembl",
organism = "Saccharomyces cerevisiae")), TRUE)
})
test_that("The is.genome.available() interface to Ensembl
works properly using taxid..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'ensembl' works properly
expect_equal(nrow(is.genome.available(db = "ensembl",
organism = "4932",
details = TRUE)) > 0, TRUE)
# test whether interface to 'ensembl' works properly without details
expect_equal(suppressMessages(is.genome.available(db = "ensembl",
organism = "4932")), TRUE)
})
test_that("The is.genome.available() interface to Ensembl
works properly using accession id", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'ensembl' works properly
expect_equal(nrow(is.genome.available(db = "ensembl",
organism = "GCA_000146045.2",
details = TRUE)) > 0, TRUE)
# test whether interface to 'ensembl' works properly without details
expect_equal(suppressMessages(is.genome.available(db = "ensembl",
organism = "GCA_000146045.2")), TRUE)
})
test_that("The is.genome.available() error messages work properly..", {
skip_on_cran()
skip_on_travis()
# test unknown organism error handling for 'refseq'
expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi",
db = "refseq")),
FALSE)
# test unknown organism error handling for 'genbank'
expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi",
db = "genbank")),
FALSE)
# test unknown organism error handling for 'ensembl'
expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi", db = "ensembl")),
FALSE)
expect_identical(suppressMessages(is.genome.available(organism = "Hrmo sapi", db = "uniprot")),
FALSE)
})
test_that("The is.genome.available() interface to Uniprot
works properly..", {
skip_on_cran()
skip_on_travis()
# test whether interface to 'uniprot' works properly
out1 <- is.genome.available(db = "uniprot",
organism = "Saccharomyces cerevisiae",
details = TRUE)
# test whether interface to 'uniprot' works properly without details
out2 <- is.genome.available(db = "uniprot",
organism = "Saccharomyces cerevisiae")
expect_true(nrow(out1) > 0)
expect_true(out2)
})
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