tests/testthat/test-manageLibraryStrategy.R

In ss-lab-cancerunit/SpiderSeqR: A Tool for Integration of Big Bio Data

context(".manageLibraryStrategy")

setSpiderSeqROption("quiet", TRUE)


#.manageLibraryStrategy("RNA", input = "syn", output = "can", mismatch.ignore = FALSE)
#.manageLibraryStrategy("RNA", input = "syn", output = "can", mismatch.ignore = TRUE)



test_that("Incorrect conversions are not allowed", {
  
  expect_error(.manageLibraryStrategy("RNA", input = "can", output = "can"))
  expect_error(.manageLibraryStrategy("RNA", input = "short", output = "short"))
  expect_error(.manageLibraryStrategy("RNA", input = "syn", output = "syn"))
  
  expect_error(.manageLibraryStrategy("RNA", input = "can", output = "syn"))
  expect_error(.manageLibraryStrategy("RNA", input = "syn", output = "short"))
  expect_error(.manageLibraryStrategy("RNA", input = "short", output = "syn"))
  expect_error(.manageLibraryStrategy("RNA", input = "short", output = "can"))
  
  
})



test_that("Conversion: can->short", {
  expect_true("RNA"==.manageLibraryStrategy("RNA-Seq", input = "can", output = "short", mismatch.ignore = FALSE))
  expect_true("ChIP"==.manageLibraryStrategy("ChIP-Seq", input = "can", output = "short", mismatch.ignore = FALSE))
  
})


test_that("Conversion: syn->can", {
  expect_true("RNA-Seq"==.manageLibraryStrategy("RNA-Seq", input = "syn", output = "can", mismatch.ignore = FALSE))
  expect_true("RNA-Seq"==.manageLibraryStrategy("RNA", input = "syn", output = "can", mismatch.ignore = FALSE))
  
})



test_that("Mismatch.ignore", {
  
  expect_error(.manageLibraryStrategy("RN", input = "syn", output = "can", mismatch.ignore = FALSE))
  expect_true("RN"==.manageLibraryStrategy("RN", input = "syn", output = "can", mismatch.ignore = TRUE))
  
  expect_error(.manageLibraryStrategy("RN", input = "can", output = "short", mismatch.ignore = FALSE))
  expect_true("RN"==.manageLibraryStrategy("RN", input = "can", output = "short", mismatch.ignore = TRUE))
  
  
})

test_that("Canonical check", {
  expect_true(.manageLibraryStrategy("ChIP-Seq", task = "check_can"))
  expect_false(.manageLibraryStrategy("ChIP", task = "check_can"))
  
  expect_true(.manageLibraryStrategy("RNA-Seq", task = "check_can"))
  expect_false(.manageLibraryStrategy("RNA", task = "check_can"))
  expect_false(.manageLibraryStrategy("sth", task = "check_can"))
  
  expect_true(.manageLibraryStrategy("WGS", task = "check_can"))
})


test_that("Canonical check", {
  
  expect_true(is.list(.manageLibraryStrategy(task = "ex")))
  expect_true(is.list(.manageLibraryStrategy(task = "ex", input = "can", output = "short")))
  expect_true(is.list(.manageLibraryStrategy(task = "ex", input = "syn", output = "can")))
  
  
})