tests/testthat/test-irfinder_parsing.R

In TRON-Bioinformatics/splice2neo: Aberrant splice junction analysis with associated mutations

test_that("parse.irfinder.txt works correctly", {
  path <-  system.file("extdata", "", package = "splice2neo")
  dat.combined <- parse_irfinder_txt(path, warnings = FALSE, irratio = 0.01, cnn=FALSE)

  expected_junc_ids <- c("chr6:96538810-96538811:+",
                         "chr6:96540534-96540535:+",
                         "chr2:231791808-231791809:+",
                         "chr2:231794262-231794263:+")
  expect_true(setequal(dat.combined$junc_id, expected_junc_ids))
  expect_true(all(dat.combined$Warnings == '-'))
  expect_true(all(dat.combined$IRratio > 0.01))

  expect_true(ncol(dat.combined) == 12)
  expect_true(nrow(dat.combined) == 4)
  expect_true(all(c("overlapping_feature", "IRratio", "Warnings", "IntronDepth") %in% colnames(dat.combined)))

})

test_that("parse.irfinder.txt works correctly with CNN input", {
  path <-  system.file("extdata", "", package = "splice2neo")
  dat.combined <- parse_irfinder_txt(path, warnings = FALSE, irratio = 0.01, cnn=TRUE)
  expect_true(ncol(dat.combined) == 12)
  expect_true(nrow(dat.combined) == 16)
  expect_true(all(c("overlapping_feature", "IRratio", "Warnings", "IntronDepth") %in% colnames(dat.combined)))

  expected_junc_ids <- c("chr1:961552-961553:+", "chr1:961628-961629:+", "chr1:961750-961751:+",
                         "chr1:961825-961826:+", "chr1:962047-962048:+", "chr1:962354-962355:+",
                         "chr1:962471-962472:+", "chr1:962703-962704:+", "chr1:963253-963254:+",
                         "chr1:963336-963337:+", "chr1:963504-963505:+", "chr1:963919-963920:+",
                         "chr1:964008-964009:+", "chr1:964106-964107:+", "chr1:999613-999614:-",
                         "chr1:999691-999692:-")
  expect_true(setequal(dat.combined$junc_id, expected_junc_ids))
  expect_true(all(dat.combined$Warnings == '-'))
  expect_true(all(dat.combined$IRratio > 0.05))

})

test_that("filter.irfinder.txt works with warnings", {

  path <-  system.file("extdata", "", package = "splice2neo")
  dat_with_warnings <- parse_irfinder_txt(path, warnings = TRUE, irratio = 0.01, cnn=FALSE)
  expect_true(ncol(dat_with_warnings) == 12)
  expect_true(nrow(dat_with_warnings) == 6)
  expect_false(all(dat_with_warnings$Warnings == "-"))

})

test_that("parse.irfinder.txt fails and returns error message when IRFinder-IR-nondir.txt is missing", {
  path <-  "."
  expect_error(parse_irfinder_txt(path))
  expect_error(parse_irfinder_txt(path, cnn=TRUE))


})