tests/testthat/test_readWrite.R

In bambu: Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

context("Generate GTF file from summarizedExperiment object")

test_that("readGTF can generate a GRangesList from a GTF file", {
    se <- readRDS(system.file("extdata", "seOutput_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds", package = "bambu"))
    gtf.file <- system.file("extdata", "Homo_sapiens.GRCh38.91_chr9_1_1000000.gtf", package = "bambu")
    path <- tempdir()
    outputGtfFile <- tempfile()
    expect_null(writeBambuOutput(se, path))
    gr <- readFromGTF(gtf.file)
    expect_null(writeToGTF(gr, outputGtfFile))

    expect_s4_class(gr, class = "CompressedGRangesList")
    expect_named(mcols(gr), c("TXNAME", "GENEID"))
})