tests/testthat/test_annotation.R

In srnadiff: Finding differentially expressed unannotated genomic regions from RNA-seq data

library(srnadiff)
library(testthat)

context("Checking annotation import")

dir     <- system.file("extdata", package="srnadiff", mustWork = TRUE)
gtfFile <- file.path(dir, "Homo_sapiens.GRCh38.76.gtf.gz")
gffFile <- file.path(dir, "mirbase21_GRCh38.gff3")

test_that("Importing miRNAs from GTF file", {
    annotation <- readAnnotation(gtfFile, source="miRNA", feature="gene")
    expect_equal(length(annotation), 164)
})

test_that("Importing precursor miRNAs from mirBase GFF3 file", {
    annotation <- readAnnotation(gffFile, feature="miRNA_primary_transcript")
    expect_equal(length(annotation), 98)
})

test_that("Importing mature miRNAs from mirBase GFF3 file", {
    annotation <- readAnnotation(gffFile, feature="miRNA")
    expect_equal(length(annotation), 161)
})

test_that("Importing non existing annotation file", {
    expect_error(readAnnotation("XXXXX.gtf"))
})