Nothing
context("gbFeatureTable getter checks")
if (getOption('biofiles.test.parser')) {
x <- getFeatures(gbRecord("sequences/nucleotide.gbk"))
} else {
load("sequences/nucleotide.rda")
x <- getFeatures(nuc)
}
test_that("Sequence, and Seqinfo can be extracted", {
expect_is(.seqinfo(x), 'seqinfo')
expect_is(.locus(x), 'gbLocus')
expect_is(.header(x), 'gbHeader')
expect_is(.sequence(x), 'DNAStringSet')
expect_is(getSequence(x), 'DNAStringSet')
})
test_that(".dbSource and .defline work for gbFeatureTables", {
expect_equal(.dbSource(x), '|gb|')
expect_match(.defline(x)[1], "lcl|.+|gb|AF229646")
})
test_that("Global accessors work for gbFeatureTables", {
expect_equal(getLocus(x), 'AF229646')
expect_equal(getLength(x), 8959)
expect_equal(getMoltype(x), 'DNA')
expect_equal(getTopology(x), 'linear')
expect_equal(getDivision(x), 'BCT')
expect_equal(getDefinition(x), 'Caulobacter crescentus pilus assembly gene cluster.')
expect_equal(getAccession(x), 'AF229646')
expect_equal(getVersion(x), 'AF229646.1')
expect_equal(getGeneID(x), '7208421')
expect_equal(getDBLink(x), NA_character_)
expect_equal(getDBSource(x), NA_character_)
expect_equal(getSource(x), 'Caulobacter crescentus CB15')
expect_equal(getOrganism(x), 'Caulobacter crescentus CB15')
expect_equal(getTaxonomy(x), 'Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Caulobacter.')
expect_equal(getOrganism(x), 'Caulobacter crescentus CB15')
expect_is(getReference(x), 'gbReferenceList')
expect_equal(getKeywords(x), '.')
expect_equal(getComment(x), NA_character_)
})
test_that("Accessors work for gbFeatureTables", {
expect_equal(index(x), 1:17)
expect_true( all(key(x) %in% c("source","gene","CDS")) )
x <- x["CDS"]
expect_true( all(key(x) %in% "CDS") )
expect_true( all(end(x) - start(x) + 1 == span(x)) )
qualifier_table <- qualif(x, c('gene','protein_id',"db_xref"))
expect_equal(dim(qualifier_table), c(8, 3))
ans1 <- .qual_access(x, 'product', TRUE, use.names=FALSE)
expect_equal(ans1[[1]], 'PilA')
expect_equal(names(ans1[[1]]), NULL)
ans2 <- .qual_access(x, 'product', TRUE, use.names=TRUE)
expect_equal(unname(ans2[[1]]), 'PilA')
expect_equal(names(ans2[[1]]), 'product')
expect_equal(.simplify(ans1),
c("PilA","CpaA","CpaB","CpaC","CpaD","CpaE","CpaF","TadB"))
expect_equal(.simplify(ans2, unlist=FALSE),
data.frame(product=c("PilA","CpaA","CpaB","CpaC","CpaD","CpaE","CpaF","TadB"),
stringsAsFactors=FALSE))
})
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