tests/testthat/test_transcriptToBiotype.R

In BgeeDB/BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation

context('testing generation of transcript to biotype file')
library(AnnotationHub)

test_that("test generation of transcript to biotype file", {
  bgee <- new("BgeeMetadata", intergenic_release = "0.1")
  kallisto <- new ("KallistoMetadata")
  user <- new("UserMetadata")
  user@species_id <- "6239" # C. elegans
  user <- setAnnotationFromFile(user, system.file("extdata", 
                                                  "annotation.gtf", 
                                                  package = "BgeeCall"), 
                                "testAnnotation")
  expect_failure(expect_error(test <- load_transcript_to_biotype(
      kallisto, bgee, user), NULL))
  expect_equal(nrow(test), 4278)
  expect_equal(ncol(test), 3)
  unlink(BgeeCall:::get_intergenic_release_path(myBgeeMetadata = bgee, 
                                                myUserMetadata = user), 
         recursive = TRUE)
  unlink(file.path(user@working_path, "release.tsv"))
})