Nothing
context("Test: getGFF()")
test_that("The getGFF() interface works properly for NCBI RefSeq (repeating command)..",{
skip_on_cran()
skip_on_travis()
# test proper download from refseq
out1 <- getGFF( db = "refseq",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE)
out2 <- getGFF( db = "refseq",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE)
expect_equal(out1, out2)
})
test_that("The getGFF() interface works properly for NCBI RefSeq using taxid (repeating command)..",{
skip_on_cran()
skip_on_travis()
# test proper download from refseq
out1 <- getGFF( db = "refseq",
organism = "559292",
path = tempdir(), mute_citation = TRUE)
out2 <- getGFF( db = "refseq",
organism = "559292",
path = tempdir(), mute_citation = TRUE)
expect_equal(out1, out2)
})
test_that("The getGFF() interface works properly for NCBI Genbank (repeating command)..",{
skip_on_travis()
skip_on_cran()
# test proper download from genbank
out1 <- getGFF( db = "genbank",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE)
out2 <- getGFF( db = "genbank",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE)
expect_equal(out1, out2)
})
test_that("The getGFF() interface works properly for Ensembl (repeating command)",{
skip_on_cran()
skip_on_travis()
# test proper download from Ensembl
out1 <- getGFF( db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE)
out2 <- getGFF( db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE)
expect_equal(out1, out2)
})
test_that("The getGTF() interface works properly for Ensembl (repeating command)",{
skip_on_cran()
skip_on_travis()
# test proper download from Ensembl
out1 <- getGTF( db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE)
out2 <- getGTF( db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE)
expect_equal(out1, out2)
})
test_that("The getGFF() interface works properly for EnsemblGenomes with collections",{
skip_on_cran()
skip_on_travis()
# Bacteria
out1 <- getGFF( db = "ensembl",
organism = "Escherichia coli",
path = tempdir(), mute_citation = TRUE)
# Fungi
out2 <- getGFF( db = "ensembl",
organism = "Acremonium chrysogenum",
path = tempdir(), mute_citation = TRUE)
# Protists
getGFF( db = "ensembl",
organism = "Babesia bigemina",
path = tempdir(), mute_citation = TRUE)
expect_false(out1 == out2)
})
test_that("The getGTF() interface works properly for EnsemblGenomes with collections",{
skip_on_cran()
skip_on_travis()
# Bacteria
out1 <- getGTF( db = "ensembl",
organism = "Escherichia coli",
path = tempdir(), mute_citation = TRUE)
# Fungi
out2 <- getGTF( db = "ensembl",
organism = "Acremonium chrysogenum",
path = tempdir(), mute_citation = TRUE)
# Protists
getGTF( db = "ensembl",
organism = "Babesia bigemina",
path = tempdir(), mute_citation = TRUE)
expect_false(out1 == out2)
})
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