tests/testthat/test_mappable.R

In coregenomics/kmap: Generate mappable regions of the genome for a given K-mer length

context("Test mappable")

## Fixtures
genome <- "BSgenome.Scerevisiae.UCSC.sacCer2"
genome_short <- tail(unlist(strsplit(genome, "\\.")), 1)
bsgenome <- BSgenome::getBSgenome(genome)
kmer <- formals(mappable)$kmer
path_cache <- tempdir()
clear_cache <- function() {
    unlink(tempdir(), recursive = TRUE)
    dir.create(tempdir())
}

test_that("mappable_cache_name returns consistent character vector", {
    success <- NULL
    try(success <- BSgenome::getBSgenome(genome_short))
    if (is.null(success))
        skip("Shorthand BSgenome names fail in non-interactive sessions")
    expect_equal(
        mappable_cache_name(bsgenome),
        mappable_cache_name(BSgenome::getBSgenome(genome_short))
    )
})

test_that("mappable_cache_name accounts for kmer", {
    mcn <- function(kmer_ = kmer, bsgenome_ = bsgenome) {
        mappable_cache_name(bsgenome_, kmer_)
    }
    expect_true(mcn(10) == mcn(10))
    expect_false(mcn(10) == mcn(11))
})

test_that("mappable validates genome name", {
    expect_error(mappable(genome = "nonsense"), "BSgenome")
    expect_error(mappable(genome = NULL), "BSgenome")
})

test_that("mappable_cache_path loads GRanges from the the file cache", {
    ## Start with an empty cache in case of any failed or interrupted tests.
    clear_cache()
    on.exit(clear_cache())
    ## Write test data to the cache.
    gr <- GRanges("chrI:1000-1200", seqinfo = Seqinfo(genome = genome_short))
    name <- mappable_cache_name(bsgenome)
    ## The file does not exist, so trying to load it should return NULL.
    expect_true(is.null(mappable_cache_load(name, bsgenome, path_cache)))
    ## Now save some data
    mappable_cache_save(gr, name, path_cache)
    ## Read from cache.
    gr_from_cache <- mappable_cache_load(name, bsgenome,
                                         cache_path = path_cache)
    mcols(gr_from_cache) <- NULL
    expect_equal(gr_from_cache, gr)

    ## Resaving should not overwrite existing data.
    mappable_cache_save(gr, name, path_cache)
    gr_from_cache <- mappable_cache_load(name, bsgenome,
                                         cache_path = path_cache)
    mcols(gr_from_cache) <- NULL
    expect_equal(gr_from_cache, gr)

    ## Multiple files of the same name in the cache should raise an error.
    mappable_cache_save(gr, name, path_cache, force = TRUE)
    expect_error(mappable(genome, cache_path = path_cache), "more than 1")
})

test_that("mappable generates and returns consistent GRanges", {
    clear_cache()
    on.exit(clear_cache())
    ## Use a subset genome for speed, otherwise Travis will kill the test.
    views <- as(bsgenome, "Views")
    end(views@granges) <- 100
    expect_message(gr_1 <- mappable(views, cache_path = path_cache),
                   "Saving result")
    expect_s4_class(gr_1, "GRanges")
    expect_message(gr_2 <- mappable(views, cache_path = path_cache),
                   "Reading the cached")
    expect_s4_class(gr_2, "GRanges")
    mcols(gr_2) <- NULL
    expect_equal(gr_2, gr_1)
})