tests/testthat/test_vcf2diem.r

In diemr: Diagnostic Index Expectation Maximisation in R

test_that("error on SNP file type", {

	filename <- system.file("extdata", "myotis.vcf", package = "diemr")
	filename2 <- as.matrix(filename)
	
  expect_error(
    object = vcf2diem(
      SNP = "filename.txt", filename = "filename"
    ),
    regexp = "should have an extension"
  )

  expect_error(
    object = vcf2diem(
      SNP = "filename.vcf", filename = "filename"
    ),
    regexp = "not found"
  )

 expect_error(
    object = vcf2diem(
      SNP = filename2, filename = "filename"
    ),
    regexp = "string with path to a vcf file"
  )
})


test_that("error on missing filename for output", {

	filename <- system.file("extdata", "myotis.vcf", package = "diemr")
	mockobject <- list(filename)
	
  expect_error(
    object = vcf2diem(
      SNP = filename
    ),
    regexp = "Provide a filename"
  )

  expect_error(
    object = vcf2diem(
      SNP = filename, filename = 1
    ),
    regexp = "Provide a filename"
  )

  expect_error(
    object = vcf2diem(
      SNP = filename, filename = mockobject
    ),
    regexp = "Provide a filename"
  )

})


test_that("incorrect chunk size", {
	
	filename <- system.file("extdata", "myotis.vcf", package = "diemr")
	
	expect_snapshot(
	     x = vcf2diem(SNP = filename, filename = "test.txt", chunk = 3)
	)
		
	expect_error(
		object = vcf2diem(SNP = c(filename, filename), filename = "test.txt", chunk = c(1:3)),
		regexp = "Provide a single object"
	)
	

})


test_that("resolve multiallelic markers", {
     
     brenthis <- system.file("extdata", "brenthis.vcf", package = "diemr")
     myotis <- system.file("extdata", "myotis.vcf", package = "diemr")
     
     expect_snapshot(
	     x = vcf2diem(SNP = brenthis, filename = "brenthis.txt", chunk = 1)
	)

    expect_snapshot(
	     x = vcf2diem(SNP = myotis, filename = "myotis.txt", chunk = 1)
	)


})