tests/testthat/test-cDNA_edge_cases.R

In andrewrech/antigen.garnish: Tumor neoantigen prediction

testthat::test_that("make_cDNA edge cases", {

  # load test data

  dt <- data.table::data.table(
    cDNA_type = c(">", ">", "ins", "del", ">", "del", "delins"),
    coding = c(LETTERS %>% paste(collapse = "")),
    cDNA_locs = c(7L, 1L, 14L, 4L, 100L, 1L, 14L),
    cDNA_locl = c(7L, 1L, 14L, 7L, 100L, 23L, 16L),
    cDNA_seq = c("*", "*", "_____", "", "*", "", "**")
  )

  # run test
  dto <- antigen.garnish:::make_cDNA(dt)

  # visually inspect
  dto[, .(coding_mut,
    coding_l = coding %>% nchar(),
    coding_mut_l = coding_mut %>% nchar(),
    ldelta = (coding_mut %>% nchar()) - (coding %>% nchar())
  )] %>% print()

  testthat::expect_equivalent(
    dto,
    data.table(structure(
      list(
        cDNA_type = c(">", ">", "ins", "del", "del", "delins"),
        coding = c(
          "ABCDEFGHIJKLMNOPQRSTUVWXYZ",
          "ABCDEFGHIJKLMNOPQRSTUVWXYZ",
          "ABCDEFGHIJKLMNOPQRSTUVWXYZ",
          "ABCDEFGHIJKLMNOPQRSTUVWXYZ",
          "ABCDEFGHIJKLMNOPQRSTUVWXYZ",
          "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
        ),
        cDNA_locs = c(
          7L,
          1L,
          14L,
          4L,
          1L,
          14L
        ),
        cDNA_locl = c(
          7L,
          1L,
          14L,
          7L,
          23L,
          16L
        ),
        cDNA_seq = c(
          "*",
          "*",
          "_____",
          "",
          "",
          "**"
        ),
        coding_mut = c(
          "ABCDEF*HIJKLMNOPQRSTUVWXYZ",
          "*BCDEFGHIJKLMNOPQRSTUVWXYZ",
          "ABCDEFGHIJKLMN_____OPQRSTUVWXYZ",
          "ABCHIJKLMNOPQRSTUVWXYZ",
          "XYZ",
          "ABCDEFGHIJKLM**QRSTUVWXYZ"
        )
      ),
      .Names = c(
        "cDNA_type",
        "coding",
        "cDNA_locs",
        "cDNA_locl",
        "cDNA_seq",
        "coding_mut"
      ),
      class = c(
        "data.table",
        "data.frame"
      )
    ))
  )
})