tests/testthat/test_one_hot_encoding_functions.R

In snikumbh/seqArchR: Identify Different Architectures of Sequence Elements

context("One-hot encoding functions")

test_that("Report empty sequence", {
  #
  testSeqsNotOK <- c()
  expect_error(get_one_hot_encoded_seqs(testSeqsNotOK),
               "Empty or NULL sequences")
  expect_error(.one_hot_encode(testSeqsNotOK, k=1),
               "Empty or NULL sequences")
})

test_that("One-hot encoding is correctly done", {
  testSeqs <- Biostrings::DNAStringSet(c("GGCT", "ATCG"))
  testSeqsB <- list(c("G", "G", "C", "T"), c("A", "T", "C", "G"))
  testAns <- t(matrix(c(
    0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 1,
    1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0
  ),
  nrow = 2, byrow = TRUE
  ))
  testAns <- Matrix::Matrix(testAns, sparse=  TRUE)
  rownames(testAns) <-
    .get_feat_names(k=1, seqlen=Biostrings::width(testSeqs[1]))
  #
  # givenAns1 <- .one_hot_encode_sinuc(testSeqsB[[1]])
  givenAns1 <- .one_hot_encode(testSeqsB[[1]], k=1)
  givenAns2 <- .one_hot_encode(testSeqsB[[2]], k=1)
  givenAns <- get_one_hot_encoded_seqs(testSeqs)
  #
  expect_is(givenAns, "dgCMatrix") ##using  Matrix
  expect_is(givenAns1, "matrix")
  expect_equal(testAns, givenAns)
})