context("Test: getCDS()")
test_that("The getCDS() interface to NCBI RefSeq works properly and skips download when file already exists..",{
skip_on_cran()
skip_on_travis()
out1 <- read_cds(getCDS( db = "refseq",
organism = "Saccharomyces cerevisiae",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
out2 <- read_cds(getCDS( db = "refseq",
organism = "Saccharomyces cerevisiae",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
expect_equal(out1, out2)
})
test_that("The getCDS() interface to NCBI RefSeq works properly with taxid (including repeating the command)..",{
skip_on_cran()
skip_on_travis()
out1 <- read_cds(getCDS( db = "refseq",
organism = "559292",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
out2 <- read_cds(getCDS( db = "refseq",
organism = "559292",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
expect_equal(out1, out2)
})
test_that("The getCDS() interface to NCBI RefSeq works properly with assembly id (including repeating the command)..",{
skip_on_cran()
skip_on_travis()
out1 <- read_cds(getCDS( db = "refseq",
organism = "GCF_000146045.2",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
out2 <- read_cds(getCDS( db = "refseq",
organism = "GCF_000146045.2",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
expect_equal(out1, out2)
})
test_that("The getCDS() interface to NCBI Genbank works properly and skips download when file already exists..",{
skip_on_cran()
skip_on_travis()
out1 <- read_cds(getCDS( db = "genbank",
organism = "Saccharomyces cerevisiae",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
out2 <- read_cds(getCDS( db = "genbank",
organism = "Saccharomyces cerevisiae",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
expect_equal(out1, out2)
})
test_that("The getCDS() interface to NCBI Genbank works properly when using taxids (including repeating the command)..",{
skip_on_cran()
skip_on_travis()
out1 <- read_cds(getCDS( db = "genbank",
organism = "559292",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
out2 <- read_cds(getCDS( db = "genbank",
organism = "559292",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
expect_equal(out1, out2)
})
test_that("The getCDS() interface to NCBI Genbank works properly when using assembly id (including repeating the command) ...",{
skip_on_cran()
skip_on_travis()
out1 <- read_cds(getCDS( db = "genbank",
organism = "GCA_000146045.2",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
out2 <- read_cds(getCDS( db = "genbank",
organism = "GCA_000146045.2",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
expect_equal(out1, out2)
})
test_that("The getCDS() throws error when wrong 'db' is selected..",{
skip_on_cran()
skip_on_travis()
expect_error(getCDS( db = "somethingelse",
organism = "Saccharomyces cerevisi",
path = tempdir(),
mute_citation = TRUE))
})
test_that("The getCDS() throws error when wrong 'organism' is selected..",{
skip_on_cran()
skip_on_travis()
expect_equal(getCDS( db = "refseq",
organism = "somethingelse",
path = tempdir(),
mute_citation = TRUE), "Not available")
})
test_that("The getCDS() interface to Ensembl skips download when file already exists..",{
skip_on_cran()
skip_on_travis()
out1 <- read_cds(getCDS( db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
out2 <- read_cds(getCDS( db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
expect_equal(out1, out2)
})
test_that("getCDS() interface to Ensembl works with taxid and skips download when file already exists..",{
skip_on_cran()
skip_on_travis()
out1 <- read_cds(getCDS( db = "ensembl",
organism = "6239",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
out2 <- read_cds(getCDS( db = "ensembl",
organism = "6239",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
expect_equal(out1, out2)
})
test_that("getCDS() interface to Ensembl works with accession id and skips download when file already exists....",{
skip_on_cran()
skip_on_travis()
out1 <- read_cds(getCDS( db = "ensembl",
organism = "GCA_000002985.3",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
out2 <- read_cds(getCDS( db = "ensembl",
organism = "GCA_000002985.3",
path = tempdir(),
mute_citation = TRUE), format = "fasta")
expect_equal(out1, out2)
})
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