tests/testthat/test-makeGRangesFromGFF-WormBase.R

In acidgenomics/freerange: Generate and Manipulate Genomic Ranges

context("makeGRangesFromGFF : WormBase")

skip_if_not(hasInternet())
file <- file.path("cache", "wormbase.gtf")

test_that("GTF genes", {
    object <- makeGRangesFromGFF(file = file, level = "genes")
    expect_s4_class(object, "GRanges")
    expect_identical(length(object), 66L)
    expect_identical(names(object)[[1L]], "WBGene00000674")
    expect_identical(
        object = lapply(mcols(object), class),
        expected = list(
            broadClass = Rle,
            geneBiotype = Rle,
            geneID = Rle,
            geneSource = Rle,
            source = Rle,
            type = Rle
        )
    )
})

test_that("GTF transcripts", {
    object <- makeGRangesFromGFF(file = file, level = "transcripts")
    expect_s4_class(object, "GRanges")
    expect_identical(length(object), 83L)
    expect_identical(names(object)[[1L]], "B0545.1a.1")
    expect_identical(
        object = lapply(mcols(object), class),
        expected = list(
            broadClass = Rle,
            geneBiotype = Rle,
            geneID = Rle,
            geneSource = Rle,
            source = Rle,
            transcriptBiotype = Rle,
            transcriptID = Rle,
            transcriptSource = Rle,
            type = Rle
        )
    )
})