tests/testthat/test_transcriptToGene.R

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

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

test_that("test generation of intergenic transcript to gene", {
  bgee <- new("BgeeMetadata", intergenic_release = "0.1")
  user <- new("UserMetadata")
  user@species_id <- "6239" # C. elegans
  expect_failure(expect_error(intergenic_txToGene <- intergenic_tx2gene(
      myBgeeMetadata = bgee, myUserMetadata = user), NULL))
  expect_equal(nrow(intergenic_txToGene), 4277)
  expect_equal(ncol(intergenic_txToGene), 2)
  unlink(BgeeCall:::get_intergenic_release_path(myBgeeMetadata = bgee, 
                                                myUserMetadata = user), 
         recursive = TRUE)
  unlink(file.path(user@working_path, "release.tsv"))
})

test_that("test creation of transcript to gene file", {
  bgee <- new("BgeeMetadata", intergenic_release = "0.1")
  kallisto <- new("KallistoMetadata")
  user <- new("UserMetadata")
  user@species_id <- "6239" # C. elegans
  user@working_path <- getwd()
  user <- setAnnotationFromFile(user, system.file("extdata", 
                                                  "annotation.gtf", 
                                                  package = "BgeeCall"), 
                                "testAnnotation")
  expect_failure(expect_error(txToGene <- read.csv(create_tx2gene(
      myAbundanceMetadata = kallisto, 
      myBgeeMetadata = bgee, 
      myUserMetadata = user), 
      header = TRUE, sep = "\t"), NULL))
  expect_equal(nrow(txToGene), 4278)
  expect_equal(ncol(txToGene), 2)
  unlink(BgeeCall:::get_intergenic_release_path(myBgeeMetadata = bgee, 
                                                myUserMetadata = user), 
         recursive = TRUE)
  unlink(file.path(user@working_path, "release.tsv"))
})