context("Test: getRNA()")
test_that(
"The getRNA() interface to NCBI RefSeq works properly (including when command is repeated)..",
{
skip_on_cran()
skip_on_travis()
# test proper download
out1 <- read_rna(
getRNA(
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_rna(
getRNA(
db = "refseq",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_equal(out1, out2)
}
)
test_that(
"The getRNA() interface to NCBI RefSeq works properly uding taxids (including when command is repeated)..",
{
skip_on_cran()
skip_on_travis()
# test proper download
out1 <- read_rna(getRNA(
db = "refseq",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta")
out2 <- read_rna(getRNA(
db = "refseq",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta")
expect_equal(out1, out2)
}
)
test_that("The getRNA() interface to NCBI RefSeq works properly using assembly ids ..",
{
skip_on_cran()
skip_on_travis()
# test proper download
out1 <- read_rna(getRNA(
db = "refseq",
organism = "GCF_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta")
out2 <- read_rna(getRNA(
db = "refseq",
organism = "GCF_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta")
expect_equal(out1, out2)
})
test_that(
"The getRNA() interface to NCBI Genbank works properly (including when command is repeated)..",
{
skip_on_cran()
skip_on_travis()
# test proper download from genbank
out1 <- read_rna(
getRNA(
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_rna(
getRNA(
db = "genbank",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_equal(out1, out2)
}
)
test_that("The getRNA() interface to NCBI Genbank works properly using taxids (including when command is repeated)..",
{
skip_on_cran()
skip_on_travis()
# test proper download from genbank
out1 <- read_rna(getRNA(
db = "genbank",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta")
out2 <- read_rna(getRNA(
db = "genbank",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta")
expect_equal(out1, out2)
})
test_that("The getRNA() interface to NCBI Genbank works properly using accession ids (including when command is repeated)..",
{
skip_on_cran()
skip_on_travis()
# test proper download from genbank
out1 <- read_rna(getRNA(
db = "genbank",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta")
out2 <- read_rna(getRNA(
db = "genbank",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta")
expect_equal(out1, out2)
})
test_that("The getRNA() interface to Ensembl works properly (including when command is repeated)..", {
skip_on_cran()
skip_on_travis()
# test proper download from ensemblgenomes
out1 <- read_rna(
getRNA(
db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
out2 <- read_rna(
getRNA(
db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_equal(out1, out2)
})
test_that("The getRNA() interface to Ensembl works properly using taxid (including when command is repeated)..", {
skip_on_cran()
skip_on_travis()
# test proper download from ensemblgenomes
# 4932
out1 <- read_rna(
getRNA(
db = "ensembl",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
out2 <- read_rna(
getRNA(
db = "ensembl",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_equal(out1, out2)
})
test_that("The getRNA() interface to Ensembl works properly using accession id (including when command is repeated)..", {
skip_on_cran()
skip_on_travis()
# test proper download from ensemblgenomes
out1 <- read_rna(
getRNA(
db = "ensembl",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
out2 <- read_rna(
getRNA(
db = "ensembl",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_equal(out1, out2)
})
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