context("detectOrganism")
with_parameters_test_that(
"Homo sapiens", {
expect_identical(
object = detectOrganism(object),
expected = "Homo sapiens"
)
},
object = c(
"Homo sapiens",
"hsapiens",
"GRCh38",
"hg38",
"ENSG00000000001",
"ENST00000000001"
)
)
with_parameters_test_that(
"Mus musculus", {
expect_identical(
object = detectOrganism(object),
expected = "Mus musculus"
)
},
object = c(
"Mus musculus",
"mmusculus",
"GRCm38",
"mm10",
"ENSMUSG00000000001",
"ENSMUST00000000001"
)
)
with_parameters_test_that(
"Rattus norvegicus", {
expect_identical(
object = detectOrganism(object),
expected = "Rattus norvegicus"
)
},
object = c(
"Rattus norvegicus",
"rnorvegicus",
"Rnor_6.0",
"rn5",
"ENSRNOG00000000001",
"ENSRNOT00000000001"
)
)
with_parameters_test_that(
"Danio rerio", {
expect_identical(
object = detectOrganism(object),
expected = "Danio rerio"
)
},
object = c(
"Danio rerio",
"drerio",
"GRCz10",
"danRer10",
"ENSDARG00000000001",
"ENSDART00000000001"
)
)
with_parameters_test_that(
"Drosophila melanogaster", {
expect_identical(
object = detectOrganism(object),
expected = "Drosophila melanogaster"
)
},
object = c(
"Drosophila melanogaster",
"dmelanogaster",
"BDGP6",
"dm6",
"FBgn0000001",
"FBtr0000001"
)
)
with_parameters_test_that(
"Caenorhabditis elegans", {
expect_identical(
object = detectOrganism(object),
expected = "Caenorhabditis elegans"
)
},
object = c(
"Caenorhabditis elegans",
"celegans",
"WBcel235",
"ce11",
"WBGene00000001"
)
)
with_parameters_test_that(
"Gallus gallus", {
expect_identical(
object = detectOrganism(object),
expected = "Gallus gallus"
)
},
object = c(
"Gallus gallus",
"ggallus",
"ENSGALG00000000001",
"ENSGALT00000000001"
)
)
with_parameters_test_that(
"Ovis aries", {
expect_identical(
object = detectOrganism(object),
expected = "Ovis aries"
)
},
object = c(
"Ovis aries",
"oaries",
"Oar_v3.1",
"oviAri3",
"ENSOARG00000000001",
"ENSOART00000000001"
)
)
## Function currently matches only the first genome.
test_that("Multiple organisms", {
expect_identical(
object = detectOrganism(c(
"ENSG00000000001",
"ENSG00000000002",
"ENSMUSG00000000001",
"ENSMUSG00000000002"
)),
expected = "Homo sapiens"
)
})
test_that("Expected failure", {
expect_error(
object = detectOrganism("XXX"),
regexp = "Failed to detect organism"
)
})
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