tests/testthat/test_misc.R

In lcolladotor/derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

test_that("Mapping levels", {
    expect_that(extendedMapSeqlevels("seq2", "UCSC", verbose = FALSE), equals("seq2"))
    expect_that(extendedMapSeqlevels("seq2", "UCSC", NULL, verbose = TRUE), shows_message("extendedMapSeqlevels: the 'seqnames' you supplied are currently not supported in GenomeInfoDb. Consider adding your genome by following the information at http://www.bioconductor.org/packages/release/bioc/vignettes/GenomeInfoDb/inst/doc/Accept-organism-for-GenomeInfoDb.pdf"))
    expect_that(extendedMapSeqlevels("seq2", "UCSC", "toy", verbose = FALSE), equals("seq2"))
    expect_that(extendedMapSeqlevels("seq2", "UCSC", "toy", verbose = TRUE), shows_message())
    expect_that(extendedMapSeqlevels("2", "toyStyle", "Arabidopsis thaliana", verbose = FALSE), equals("2"))
    expect_that(extendedMapSeqlevels("2", "toyStyle", "Arabidopsis thaliana", verbose = TRUE), shows_message())
    expect_that(extendedMapSeqlevels("2", "NCBI", "Arabidopsis thaliana", "toyStyle", verbose = FALSE), equals("2"))
    expect_that(extendedMapSeqlevels("2", "NCBI", "Arabidopsis thaliana", "toyStyle", verbose = TRUE), shows_message(""))
    expect_that(extendedMapSeqlevels("2", "UCSC", "Homo sapiens", "NCBI"), equals("chr2"))
    expect_that(extendedMapSeqlevels("2", "UCSC", "Homo sapiens", verbose = TRUE), shows_message("extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens"))
    expect_that(extendedMapSeqlevels("2", "UCSC", "Homo sapiens", "NCBI"), equals(extendedMapSeqlevels("2", "UCSC", "Homo sapiens", verbose = FALSE)))
    expect_that(extendedMapSeqlevels("2", "UCSC", "Homo sapiens", "NCBI"), equals(extendedMapSeqlevels("2", "UCSC", "homo_saPiens", "NcBI")))
    expect_that(extendedMapSeqlevels("28", NULL), equals("28"))
    expect_that(extendedMapSeqlevels("T", "NCBI", "homo_sapiens"), shows_message())
    expect_that(extendedMapSeqlevels("T", "NCBI", "homo_sapiens", verbose = FALSE), equals("T"))
    expect_that(extendedMapSeqlevels("T", "NCBI", NULL, verbose = FALSE), equals("LGI"))
})


foo <- function(...) {
    derfinder::define_cluster(...)
}
fuu <- function(...) {
    cores <- derfinder:::.advanced_argument("cores", 1L, ...)
    derfinder::define_cluster(cores = "test", test = cores)
}

library("BiocParallel")
test_that("Cluster setup", {
    expect_that(foo(), equals(SerialParam()))
    expect_equal(foo(mc.cores = 2), SnowParam(2, log = TRUE), tolerance = 0.1)
    expect_that(foo(), equals(fuu()))
    expect_equal(fuu(cores = 4), SnowParam(4, log = TRUE), tolerance = 0.1)
})