Nothing
context("gbRecord parser checks (GenBank files)")
if (getOption('biofiles.test.parser')) {
#nuc.efetch <- reutils::efetch('457866357', 'nuccore', 'gb')
#save(nuc.efetch, file = "sequences/nuc.efetch.RData")
load("sequences/nuc.efetch.RData")
nuc.efetch <- gbRecord(nuc.efetch)
nuc <- gbRecord("sequences/nucleotide.gbk")
} else {
#save(nuc.efetch, file = "sequences/nuc.efetch.rda")
load("sequences/nuc.efetch.rda")
load("sequences/nucleotide.rda")
}
test_that("GenBank records parse correctly from file and efetch", {
expect_is(nuc, 'gbRecord')
expect_is(nuc.efetch, 'gbRecord')
expect_is(gbRecordList(nuc, nuc.efetch), 'gbRecordList')
})
test_that("Feature list, Sequence, and Seqinfo can be extracted", {
expect_is(.locus(nuc@seqinfo), 'gbLocus')
expect_is(.locus(nuc), 'gbLocus')
expect_is(.header(nuc@seqinfo), 'gbHeader')
expect_is(.header(nuc), 'gbHeader')
expect_is(.sequence(nuc@seqinfo), 'DNAStringSet')
expect_is(.sequence(nuc), 'DNAStringSet')
expect_is(.features(nuc), 'gbFeatureTable')
expect_identical(.contig(nuc), NULL)
})
test_that(".dbSource and .defline work for gbRecords", {
expect_equal(.dbSource(nuc), '|gb|')
expect_equal(.defline(nuc),
"gi|7208421|gb|AF229646 Caulobacter crescentus pilus assembly gene cluster.")
})
test_that("Accessors work for GenBank records", {
expect_equal(getAccession(nuc), "AF229646")
expect_equal(getGeneID(nuc), "7208421")
expect_equal(getLength(nuc), 8959)
expect_equal(getDefinition(nuc), "Caulobacter crescentus pilus assembly gene cluster.")
expect_true( all(end(nuc) - start(nuc) + 1 == span(nuc)) )
expect_equal(unique(strand(nuc)), 1)
expect_is(qualifList(nuc), 'list')
})
context("gbRecord parser checks (GenPept files)")
if (getOption('biofiles.test.parser')) {
#prot.efetch <- reutils::efetch(c('459479542','379049216'), 'protein', 'gp')
#save(prot.efetch, file = "sequences/prot.efetch.RData")
load("sequences/prot.efetch.RData")
prot.efetch <- gbRecord(prot.efetch)
prot <- gbRecord("sequences/protein.gp")
} else {
#save(prot.efetch, file = "sequences/prot.efetch.rda")
#save(prot, file = "sequences/protein.rda")
load("sequences/prot.efetch.rda")
load("sequences/protein.rda")
}
test_that("GenPept records parse correctely from file and efetch", {
expect_is(prot, 'gbRecord')
expect_is(prot.efetch, 'gbRecordList')
expect_is(gbRecordList(prot, prot.efetch), "gbRecordList")
})
test_that("Feature list, Sequence, and Seqinfo can be extracted", {
expect_is(.locus(prot@seqinfo), 'gbLocus')
expect_is(.locus(prot), 'gbLocus')
expect_is(.header(prot@seqinfo), 'gbHeader')
expect_is(.header(prot), 'gbHeader')
expect_is(.sequence(prot@seqinfo), 'AAStringSet')
expect_is(.sequence(prot), 'AAStringSet')
expect_is(.features(prot), 'gbFeatureTable')
expect_identical(.contig(prot), NULL)
})
test_that(".dbSource and .defline work", {
expect_equal(.dbSource(prot), '|gb|')
expect_equal(.defline(prot),
"gi|404302394|gb|EJZ56356 CpaF [Pseudomonas fluorescens R124].")
expect_equal(.dbSource(prot.efetch), c('|gb|', '|gb|'))
})
context("gbRecord parser checks (Embl files)")
if (getOption('biofiles.test.parser')) {
nuc <- gbRecord("sequences/sample.embl")
test_that("Emble records parse correctly from file", {
expect_is(nuc, 'gbRecord')
})
test_that("Feature list, Sequence, and Seqinfo can be extracted", {
expect_is(.locus(nuc@seqinfo), 'gbLocus')
expect_is(.locus(nuc), 'gbLocus')
expect_is(.header(nuc@seqinfo), 'gbHeader')
expect_is(.header(nuc), 'gbHeader')
expect_is(.sequence(nuc@seqinfo), 'DNAStringSet')
expect_is(.sequence(nuc), 'DNAStringSet')
expect_is(.features(nuc), 'gbFeatureTable')
expect_identical(.contig(nuc), NULL)
})
test_that("Accessors work for GenBank records", {
expect_equal(getAccession(nuc), c("X56734", "S46826"))
expect_equal(getGeneID(nuc), NA_character_)
expect_equal(getLength(nuc), 1859)
expect_equal(getDefinition(nuc), "Trifolium repens mRNA for non-cyanogenic beta-glucosidase")
expect_true( all(end(nuc) - start(nuc) + 1 == span(nuc)) )
expect_equal(unique(strand(nuc)), 1)
expect_is(qualifList(nuc), 'list')
})
}
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