Nothing
context("Test: getGenome()")
test_that("The getGenome() interface works properly for NCBI RefSeq (including when command is repeated)..", {
skip_on_cran()
skip_on_travis()
# test proper download from genbank
out1 <- read_genome(
getGenome(
db = "refseq",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
# test proper use of internal referece files when command is repeated
out2 <- read_genome(
getGenome(
db = "refseq",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_s4_class(out1, class = "DNAStringSet")
expect_false(any(out1 != out2))
})
test_that("The getGenome() interface works properly for NCBI RefSeq using taxid..", {
skip_on_cran()
skip_on_travis()
# test proper download from genbank
out1 <- read_genome(
getGenome(
db = "refseq",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_s4_class(out1, class = "DNAStringSet")
})
test_that("The getGenome() interface works properly for NCBI RefSeq using assembly id..", {
skip_on_cran()
skip_on_travis()
# test proper download from genbank
out1 <- read_genome(
getGenome(
db = "refseq",
organism = "GCF_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_s4_class(out1, class = "DNAStringSet")
})
test_that("The getGenome() interface works properly for NCBI Genbank (including when command is repeated)..", {
skip_on_cran()
skip_on_travis()
# test proper download from genbank
out1 <- read_genome(
getGenome(
db = "genbank",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
# test proper use of internal referece files when command is repeated
out2 <- read_genome(
getGenome(
db = "genbank",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_s4_class(out1, class = "DNAStringSet")
expect_false(any(out1 != out2))
})
test_that("The getGenome() interface works properly for NCBI Genbank using taxid (including when command is repeated)..", {
skip_on_cran()
skip_on_travis()
# test proper download from genbank
out1 <- read_genome(
getGenome(
db = "genbank",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
# test proper use of internal referece files when command is repeated
out2 <- read_genome(
getGenome(
db = "genbank",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_s4_class(out1, class = "DNAStringSet")
expect_false(any(out1 != out2))
})
test_that("The getGenome() interface works properly for NCBI Genbank using accession ids (including when command is repeated)..", {
skip_on_cran()
skip_on_travis()
# test proper download from genbank
out1 <- read_genome(
getGenome(
db = "genbank",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
# test proper use of internal referece files when command is repeated
out2 <- read_genome(
getGenome(
db = "genbank",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_s4_class(out1, class = "DNAStringSet")
expect_false(any(out1 != out2))
})
test_that("The getGenome() interface works properly for ENSEMBL (including repeating function call)..",{
skip_on_cran()
skip_on_travis()
# test proper download from ENSEMBL
out1 <- read_genome(
getGenome(
db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
out2 <- read_genome(
getGenome(
db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_s4_class(out1, class = "DNAStringSet")
expect_false(any(out1 != out2))
})
test_that("The getGenome() interface works properly for ENSEMBL using taxid (including repeating function call)..",{
skip_on_cran()
skip_on_travis()
# test proper download from ENSEMBL
out1 <- read_genome(
getGenome(
db = "ensembl",
organism = "4932",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
out2 <- read_genome(
getGenome(
db = "ensembl",
organism = "4932",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_s4_class(out1, class = "DNAStringSet")
expect_false(any(out1 != out2))
})
test_that("The getGenome() interface works properly for ENSEMBL using accession id (including repeating function call)..",{
skip_on_cran()
skip_on_travis()
# test proper download from ENSEMBL
out1 <- read_genome(
getGenome(
db = "ensembl",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
out2 <- read_genome(
getGenome(
db = "ensembl",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_s4_class(out1, class = "DNAStringSet")
expect_false(any(out1 != out2))
})
test_that("The getGenome() interface works properly for ENSEMBL with collections",{
skip_on_cran()
skip_on_travis()
# test proper download from ENSEMBL
# Bacteria
out1 <- getGenome(db = "ensembl",
organism = "Escherichia coli",
path = tempdir(), mute_citation = TRUE)
# Fungi
out2 <- getGenome(db = "ensembl",
organism = "Acremonium chrysogenum",
path = tempdir(), mute_citation = TRUE)
# Protists
getGenome(db = "ensembl",
organism = "Babesia bigemina",
path = tempdir(), mute_citation = TRUE)
expect_false(out1 == out2)
})
test_that("The getGenome() error messages work properly for ENSEMBL..", {
skip_on_cran()
skip_on_travis()
out1 <- getGenome(
db = "ensembl",
organism = "Saccharomycesi",
path = tempdir(), mute_citation = TRUE
)
expect_type(out1, "logical")
expect_false(out1 == TRUE)
})
test_that("The getGenome() error messages work properly for NCBI RefSeq", {
skip_on_cran()
skip_on_travis()
expect_equal(getGenome(
db = "refseq",
organism = "Saccharomycesi",
path = tempdir(), mute_citation = TRUE
), "Not available")
})
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