tests/testthat/test_consensusMatrix.R

In philliplab/yasss: Yet Another Short Sequence Simulator

context("consensusMatrix")

x <- sample(c('A','C','G','T'), 50, replace = TRUE)
x <- matrix(x, ncol = 5, nrow = 10)
seqs <- apply(x, 1, paste, sep = '', collapse = '')


test_that("consensusMatrix works", {
  cm <- consensusMatrix_character(seqs)
  the_rownames <- c("A", "C", "G", "T", "M", "R", "W", "S", "Y", "K", "V", "H",
                    "D", "B", "N", "-", "+", ".")
  expect_equal(attr(cm, "dimnames")[[1]], the_rownames)

  expect_equal(min(apply(cm, 2, sum)), max(apply(cm, 2, sum)))
  expect_equal(min(apply(cm, 2, sum)), 10)

  expect_equal(dim(cm), c(18, 5))

})

test_that("consensusMatrx_character do not confuse rows and columns", {
  seqs <- c('AAAA', 'CCCC')
  cm <- consensusMatrix_character(seqs)

  expect_true(all(cm[1:2,1:4] == 1))
  
  seqs <- c('AACC', 'AACC')
  cm <- consensusMatrix_character(seqs)

  expect_true(all(cm[1,1:2] == 2))
  expect_true(all(cm[2,3:4] == 2))
})