context("Test: getAssemblyStats()")
test_that("The getAssemblyStats() downloads assembly stats file and reads
raw input: NCBI RefSeq ..",{
skip_on_cran()
skip_on_travis()
library(magrittr)
Scerevisiae.stats <- getAssemblyStats(
db = "refseq",
organism = "Saccharomyces cerevisiae",
path = tempdir(),
mute_citation = TRUE
)
raw <- Scerevisiae.stats %>%
read_assemblystats(type = "raw")
stats <- Scerevisiae.stats %>%
read_assemblystats(type = "stats")
expect_false(nrow(raw) == nrow(stats))
})
test_that("The getAssemblyStats() downloads assembly stats file and reads raw
input: NCBI Genbank ..",{
skip_on_cran()
skip_on_travis()
Scerevisiae.stats <- getAssemblyStats(
db = "genbank",
organism = "Saccharomyces cerevisiae",
path = tempdir(),
mute_citation = TRUE
)
raw <- read_assemblystats(Scerevisiae.stats, type = "raw")
stats <- read_assemblystats(Scerevisiae.stats, type = "stats")
expect_false(nrow(raw) == nrow(stats))
})
test_that("The getAssemblyStats() downloads assembly stats file and imports file
..",{
skip_on_cran()
skip_on_travis()
Scerevisiae.stats <- getAssemblyStats(
db = "refseq",
organism = "Saccharomyces cerevisiae",
type = "import",
path = tempdir(),
mute_citation = TRUE
)
expect_false(nrow(Scerevisiae.stats) == 0)
})
test_that("The getAssemblyStats() throws error when undefined 'type' is selected
..",{
skip_on_cran()
skip_on_travis()
expect_error(getAssemblyStats(
db = "refseq",
organism = "Saccharomyces cerevisiae",
type = "somethingelse",
path = tempdir(),
mute_citation = TRUE))
})
test_that("The getAssemblyStats() throws error when undefined 'db' is selected
..",{
skip_on_cran()
skip_on_travis()
expect_error(getAssemblyStats(
db = "somethingelse",
organism = "Saccharomyces cerevisiae",
type = "download",
path = tempdir(),
mute_citation = TRUE))
})
test_that("The getAssemblyStats() throws error when undefined 'organism' is selected
..",{
skip_on_cran()
skip_on_travis()
expect_message(getAssemblyStats(
db = "refseq",
organism = "somethingelse",
type = "download",
path = tempdir(),
mute_citation = TRUE))
})
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