context("Test: getProteome()")
test_that("The getProteome() interface to NCBI RefSeq works properly (including repeating command)..", {
skip_on_cran()
skip_on_travis()
# test proper download
out1 <-
read_proteome(
getProteome(
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_proteome(
getProteome(
db = "refseq",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_false(length(out1) != length(out2) | length(out1) == 0)
})
test_that("The getProteome() interface to NCBI RefSeq works properly using taxid (including repeating command)..", {
skip_on_cran()
skip_on_travis()
# test proper download
out1 <- read_proteome(
getProteome(
db = "refseq",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
# test proper use of internal referece files when command is repeated
out2 <- read_proteome(
getProteome(
db = "refseq",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_false(length(out1) != length(out2) | length(out1) == 0)
})
test_that("The getProteome() interface to NCBI RefSeq works properly using accession id (including repeating command)..", {
skip_on_cran()
skip_on_travis()
# test proper download
out1 <- read_proteome(
getProteome(
db = "refseq",
organism = "GCF_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
# test proper use of internal referece files when command is repeated
out2 <- read_proteome(
getProteome(
db = "refseq",
organism = "GCF_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_false(length(out1) != length(out2) | length(out1) == 0)
})
test_that("The getProteome() interface to NCBI Genbank works properly (including repeating command)..", {
skip_on_cran()
skip_on_travis()
# test proper download from genbank
out1 <- read_proteome(
getProteome(
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_proteome(
getProteome(
db = "genbank",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_false(length(out1) != length(out2) | length(out1) == 0)
})
test_that("The getProteome() interface to NCBI Genbank works properly using taxid (including repeating command)..", {
skip_on_cran()
skip_on_travis()
# test proper download
out1 <- read_proteome(
getProteome(
db = "genbank",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
# test proper use of internal referece files when command is repeated
out2 <- read_proteome(
getProteome(
db = "genbank",
organism = "559292",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_false(length(out1) != length(out2) | length(out1) == 0)
})
test_that("The getProteome() interface to NCBI Genbank works properly using accession (including repeating command)..", {
skip_on_cran()
skip_on_travis()
# test proper download
out1 <- read_proteome(
getProteome(
db = "genbank",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
# test proper use of internal referece files when command is repeated
out2 <- read_proteome(
getProteome(
db = "genbank",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_false(length(out1) != length(out2) | length(out1) == 0)
})
test_that("The getProteome() interface to Ensembl works properly (including repeating command)..", {
skip_on_cran()
skip_on_travis()
out1 <- read_proteome(
getProteome(
db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
out2 <- read_proteome(
getProteome(
db = "ensembl",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_false(length(out1) != length(out2) | length(out1) == 0)
})
test_that("The getProteome() interface to Ensembl works properly using taxid (including repeating command)..", {
skip_on_cran()
skip_on_travis()
out1 <- read_proteome(
getProteome(
db = "ensembl",
organism = "4932",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
out2 <- read_proteome(
getProteome(
db = "ensembl",
organism = "4932",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_false(length(out1) != length(out2) | length(out1) == 0)
})
test_that("The getProteome() interface to Ensembl works properly using accession ids (including repeating command)..", {
skip_on_cran()
skip_on_travis()
out1 <- read_proteome(
getProteome(
db = "ensembl",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
out2 <- read_proteome(
getProteome(
db = "ensembl",
organism = "GCA_000146045.2",
path = tempdir(), mute_citation = TRUE
),
format = "fasta"
)
expect_false(length(out1) != length(out2) | length(out1) == 0)
})
test_that("The getProteome() interface to Ensembl works properly (For organisms with collections)..", {
skip_on_cran()
skip_on_travis()
out <- getProteome(
db = "ensembl",
organism = "Escherichia coli",
path = tempdir(), mute_citation = TRUE
)
expect_false(is.logical(out))
})
test_that("The getProteome() interface to Uniprot works properly ..", {
skip_on_cran()
skip_on_travis()
out1 <- getProteome(
db = "uniprot",
organism = "Saccharomyces cerevisiae",
path = tempdir(), mute_citation = TRUE
)
out2 <- getProteome(
db = "uniprot",
organism = "Homo sapiens",
path = tempdir(), mute_citation = TRUE
)
expect_false(is.logical(c(out1, out2)))
expect_false(anyNA(c(out1, out2)))
expect_false(identical(out1, out2))
})
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