tests/testthat/test-makeGRangesFromGFF-GENCODE.R

In acidgenomics/freerange: Generate and Manipulate Genomic Ranges

context("makeGRangesFromGFF : GENCODE")

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

test_that("GTF genes", {
    object <- makeGRangesFromGFF(file = file, level = "genes")
    expect_s4_class(object, "GRanges")
    expect_identical(length(object), 60L)
    expect_identical(names(object)[[1L]], "ENSG00000177757.2")
    expect_identical(
        object = lapply(mcols(object), class),
        expected = list(
            broadClass = Rle,
            geneBiotype = Rle,
            geneID = Rle,
            geneName = Rle,
            havanaGene = Rle,
            level = Rle,
            source = Rle,
            tag = Rle,
            type = Rle
        )
    )
})

test_that("GTF transcripts", {
    object <- makeGRangesFromGFF(file = file, level = "transcripts")
    expect_s4_class(object, "GRanges")
    expect_identical(length(object), 167L)
    expect_identical(names(object)[[1L]], "ENST00000326734.2")
    expect_identical(
        object = lapply(mcols(object), class),
        expected = list(
            broadClass = Rle,
            ccdsID = Rle,
            geneBiotype = Rle,
            geneID = Rle,
            geneName = Rle,
            havanaGene = Rle,
            havanaTranscript = Rle,
            level = Rle,
            ont = Rle,
            proteinID = Rle,
            source = Rle,
            tag = Rle,
            transcriptBiotype = Rle,
            transcriptID = Rle,
            transcriptName = Rle,
            transcriptSupportLevel = Rle,
            type = Rle
        )
    )
})

file <- file.path("cache", "gencode.gff3")

test_that("GFF3 genes", {
    object <- makeGRangesFromGFF(file = file, level = "genes")
    expect_s4_class(object, "GRanges")
    expect_identical(length(object), 60L)
    expect_identical(names(object)[[1L]], "ENSG00000177757.2")
    expect_identical(
        object = lapply(mcols(object), class),
        expected = list(
            broadClass = Rle,
            geneBiotype = Rle,
            geneID = Rle,
            geneName = Rle,
            havanaGene = Rle,
            level = Rle,
            source = Rle,
            type = Rle
        )
    )
})

test_that("GFF3 transcripts", {
    object <- makeGRangesFromGFF(file = file, level = "transcripts")
    expect_s4_class(object, "GRanges")
    expect_identical(length(object), 167L)
    expect_identical(names(object)[[1L]], "ENST00000326734.2")
    expect_identical(
        object = lapply(mcols(object), class),
        expected = list(
            broadClass = Rle,
            ccdsID = Rle,
            geneBiotype = Rle,
            geneID = Rle,
            geneName = Rle,
            havanaGene = Rle,
            havanaTranscript = Rle,
            level = Rle,
            proteinID = Rle,
            source = Rle,
            transcriptBiotype = Rle,
            transcriptID = Rle,
            transcriptName = Rle,
            transcriptSupportLevel = Rle,
            type = Rle
        )
    )
})