Nothing
context("Feature parser checks")
src1 <- readLines("sequences/source.gbk")
cds1 <- readLines("sequences/CDS.gbk")
test_that("GenBank feature tables parse correctly", {
expect_is(gbFeature(src1), 'gbFeature')
expect_is(gbFeature(cds1), 'gbFeature')
})
src2 <- readLines("sequences/source.embl")
cds2 <- readLines("sequences/CDS.embl")
test_that("Embl feature tables parse correctly", {
expect_is(gbFeature(src2), 'gbFeature')
expect_is(gbFeature(cds2), 'gbFeature')
})
context("gbFeature getter/setter checks")
test_that("gbFeature accessors work", {
x <- biofiles:::gbFeature(cds2, id = 10)
expect_is(biofiles:::.seqinfo(x), "seqinfo")
expect_is(biofiles:::.header(x), "gbHeader")
expect_is(biofiles:::.locus(x), "gbLocus")
expect_is(biofiles:::.sequence(x), "BStringSet")
## index
expect_equal(index(x), 10)
## key
expect_equal(key(x), 'CDS')
expect_equal(x[['key']], 'CDS')
## location
expect_equal(start(x), 14)
expect_equal(end(x), 1495)
expect_equal(span(x), 1482)
expect_equal(strand(x), 1)
expect_equal(joint_range(x), c(14, 1495))
expect_equal(fuzzy(x), matrix(c(FALSE, FALSE), nrow = 1))
expect_output(show(location(x)), "14..1495")
expect_output(show(x[['location']]), "14..1495")
x <- biofiles:::gbFeature(cds1, id = 10)
## specific qualifiers
expect_equal(locusTag(x), "STMUK_0002")
expect_equal(geneID(x), "thrA")
expect_equal(product(x), "bifunctional aspartokinase I/homoserine dehydrogenase I")
expect_equal(proteinID(x), "AEF05936.1")
expect_is(note(x), "character")
expect_is(translation(x), "AAStringSet")
## db_xrefs returns named character vector or NA if a db is not present
expect_equal(dbxref(x), c(db_xref.taxon = "990282", db_xref.GI = "332986953"))
expect_equal(dbxref(x, "GI"), c(db_xref.GI = "332986953"))
expect_equal(dbxref(x, "foo"), c(db_xref.foo = NA_character_))
# qualif returns named character vector or NA if a db is not present
expect_equal(qualif(x, 'locus_tag'), c(locus_tag = 'STMUK_0002'))
# get more than one qualifier
expect_equal(qualif(x, c("locus_tag", "gene")), c(locus_tag = "STMUK_0002", gene = "thrA"))
expect_equal(qualif(x, "foo"), c(foo = NA_character_))
})
test_that("gbFeature replacement methods work", {
x <- biofiles:::gbFeature(cds1, id = 10)
## replace start
start(x) <- 100
expect_equal(start(x), 100)
## replace end
end(x) <- 200
expect_equal(end(x), 200)
## try to make start > end
expect_error(start(x) <- 300)
## try again, switching off validity checks
start(x, check = FALSE) <- 300
expect_is(location(x), "gbLocation")
## replace key
## Should we check for valid keys?
key(x) <- "FOO"
expect_equal(key(x), "FOO")
## replace qulifier
qualif(x, "gene") <- "bar"
expect_equal(qualif(x, "gene"), c(gene = "bar"))
## try replacing qualifier without specifying which
expect_error(qualif(x) <- "baz")
})
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.