tests/testthat/test-make_cDNA.R

In andrewrech/antigen.garnish: Tumor neoantigen prediction

testthat::test_that("make_cDNA", {

  # load test data
  dt <- data.table::data.table(
    cDNA_type = c(">", ">"),
    coding = c(
      "ATGGCAGAGTTCTCCCAGAAGCAGAGGAAACAGAGCGGCAGCGAGGGCCTGGGCAGTGTGGTGGACTTCCTCTTGGCTAATGCTCGATTGGTGCTAGGTGTGGGCGGGGCTGCAGTGCTGGGCATTGCTACCCTGGCTGTAAAGCGGCTCATCGACAGGGCCACCAGCCCTCCAGATGAGGATGACACCAAGGGGGACAGCTGGAAGGAACTGAGCCTGCTGAGAGCCACATCGCCCCAAAAGCCCCAACCCCCTCCTGCTGCCTTCAGCCAGCCCCTAGCTACTGGGTCCCCCTCCCCCTCTGTGCCAGTGGAGCCCACGCCCATTCATTCTCCCACGACACCTAAGTTCAGCACTATAGCACCCCTGTGCCTGACGTTCCAGGAGAGGCTGCTGGCCTTCGAGCGCAAGCATGTGATTACCCCAGAAGCCCACGTGACGTTGGCGAAACAGCTGGCTGGAGACATTGCCTTGGAGCTGCAGGCCTACTTGAGGAGCAAGTTCCCAGAACTGCCCTTTGGTGCACTCGTGCCGGGTGGGCCTCTCTACGACGGGCTCCAGGCAGGGACTGCTGAGCACGTGCGCCTGCTGGCGCCTCTGGAGTTGGAGCCGGGGCTATGGAGCCTGGTACCTGGCGTGGACACTGTGGCCAGGGAGCCTCGATGCTGGGCTGTACGCAGGACTCAGCTTGAGTTTCATCCCCGTGGGTGCAGCCCATGGGACCGCTTCCTGGTGGGGGGCTACCTCTCCTCCCGAGTCTTGCTGGAGCTGCTACGGAAGGCCCTGTCAGCCTCTGTCAACTGGCCAGCCATTGGCAGCCTGCTCGGGTGTCTGATCTGGCCCGATGTGGCTTCGGAGGAGCTGCTGCTCAAAGTGCAACACGAGTGCCTGGAGTTCACTTTAGCTGTGCTCATGGTAGTCCCTGGGGCCAGCACTGATGACCGCCTGCTGCTGGCTTGGCCCCTAGAGGGGCTGGCCAGCAATCTCTGGCTGCAGGATCTATATCCAGTAGAGACCGCCCGTTTGCGGGCCCTGGATGACCAGGATGCTGGTACTCGGCGGAGGTTGTTGCTGCTGCTGTGTGGTATCTGTCGTGGCCATCCGGCTCTAGTGCGGCTGGGCTGGAGCCACCTGACTCAGGTGGTTCTGCATCTGGGTGAAGAGGAAGTGGCCTGGACTGAGGAGGCCTTGGGGGAACGGTTTCTGCAAGCCCTGGAGTTTCTGGTGGGCAGCTTGGAGCAGGCTAGCCTGCCCTGTCACTTCAACCCCAGTGTGAACCTCTTGGGTAACTTCCGGGAAGAGGAGATTGATGACATTGGCTACGTGCTGTACAGCGGCCTCCAGGTTCCTGAAAGCCTATTCTAG",
      "ATGGCGGCCGCCAGCGGCTACACCGACCTGCGGGAGAAGCTCAAGTCCATGACGTCCCGGGACAACTACAAGGCGGGCAGTCGGGAGGCCGCCGCCGCTGCGGCCGCCGCCGTGGCTGCCGCTGCCGCTGCCGCGGCCGCCGCTGAGCCTTACCCGGCGTCCGGGACCACCAAGCGGAAATACCAGGAGGACTCGGACCCCGAGCGCAGCGACTACGAGGAGCATCAGTTGCAGAAGGAGGAAGAGGCGCGCAAGGTGAAGAGCGGCATCCGGCAGATCCGGCTCTTCAGTCAGGATGAGTGCTCCAAGATCGAGGCCCGCATCGATGAGGTGGTGTCCCGCGCCGAGAAGGGCCTGTACAACGAGCACACGGTGGACCGGGCCCCCCTGCGCAACAAGTACTTCTTCGGCGAGGGCTACACGTACGGGGCCCAGCTGCAGAAGCGCGGGCCGGGCCAGGAGCGCCTCTACCCGCCGGGCGACGTCGACGAGATCCCGGACTGGGTGCATCAGCTGGTGATCCAGAAGCTGGTGGAGCACCGCGTCATCCCCGAGGGCTTCGTCAACAGCGCGGTCATCAACGACTACCAGCCCGGCGGCTGCATCGTGTCCCACGTTGACCCCATCCACATCTTCGAGCGCCCCATCGTGTCCGTGTCTTTCTTCAGCGACTCGGCACTTTGCTTCGGCTGCAAGTTCCAGTTCAAGCCCATCCGGGTGTCGGAACCTGTGCTTTCTCTGCCGGTGCGCAGGGGGAGCGTGACTGTGCTCAGTGGGTATGCTGCTGATGAAATCACTCACTGCATACGGCCTCAGGACATTAAGGAACGCCGGGCGGTCATCATTCTCAGGAAGACAAGATTAGATGCACCGCGATTGGAAACAAAATCCCTGAGCAGCTCCACATTGCCACCCAGCTATGCTTCAGATCGCCTGTCAGGAAACACCAGAGACCCTGCGCTGAAACCCAAAAGGTCCCACCGCAAGGCAGACCCTGATGCTGCCCACAGGCCCCGGATCCTGGAAATGGACAAAGAAGAAAACCGGCGGTCTGTGCTCCTGCCCACACACCGGCGGAGGGGGAGTTTTAGCTCTGAGAACTATTGGCGCAAATCCTATGAGTCCTCGGAAGATTGCCCAGAGGCAGCCAGCAGCCCCACCCGCAAGGTGAAGATGAGGAGACACTGA"
    ),
    cDNA_locs = c(718L, 1114L),
    cDNA_locl = c(718L, 1114L),
    cDNA_seq = c("A", "G")
  )

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

  testthat::expect_equal(
    dto$coding_mut,
    c(
      "ATGGCAGAGTTCTCCCAGAAGCAGAGGAAACAGAGCGGCAGCGAGGGCCTGGGCAGTGTGGTGGACTTCCTCTTGGCTAATGCTCGATTGGTGCTAGGTGTGGGCGGGGCTGCAGTGCTGGGCATTGCTACCCTGGCTGTAAAGCGGCTCATCGACAGGGCCACCAGCCCTCCAGATGAGGATGACACCAAGGGGGACAGCTGGAAGGAACTGAGCCTGCTGAGAGCCACATCGCCCCAAAAGCCCCAACCCCCTCCTGCTGCCTTCAGCCAGCCCCTAGCTACTGGGTCCCCCTCCCCCTCTGTGCCAGTGGAGCCCACGCCCATTCATTCTCCCACGACACCTAAGTTCAGCACTATAGCACCCCTGTGCCTGACGTTCCAGGAGAGGCTGCTGGCCTTCGAGCGCAAGCATGTGATTACCCCAGAAGCCCACGTGACGTTGGCGAAACAGCTGGCTGGAGACATTGCCTTGGAGCTGCAGGCCTACTTGAGGAGCAAGTTCCCAGAACTGCCCTTTGGTGCACTCGTGCCGGGTGGGCCTCTCTACGACGGGCTCCAGGCAGGGACTGCTGAGCACGTGCGCCTGCTGGCGCCTCTGGAGTTGGAGCCGGGGCTATGGAGCCTGGTACCTGGCGTGGACACTGTGGCCAGGGAGCCTCGATGCTGGGCTGTACGCAGGACTCAGCTTGAGTTTCATCCCCGTGGGTGCAGCCCAAGGGACCGCTTCCTGGTGGGGGGCTACCTCTCCTCCCGAGTCTTGCTGGAGCTGCTACGGAAGGCCCTGTCAGCCTCTGTCAACTGGCCAGCCATTGGCAGCCTGCTCGGGTGTCTGATCTGGCCCGATGTGGCTTCGGAGGAGCTGCTGCTCAAAGTGCAACACGAGTGCCTGGAGTTCACTTTAGCTGTGCTCATGGTAGTCCCTGGGGCCAGCACTGATGACCGCCTGCTGCTGGCTTGGCCCCTAGAGGGGCTGGCCAGCAATCTCTGGCTGCAGGATCTATATCCAGTAGAGACCGCCCGTTTGCGGGCCCTGGATGACCAGGATGCTGGTACTCGGCGGAGGTTGTTGCTGCTGCTGTGTGGTATCTGTCGTGGCCATCCGGCTCTAGTGCGGCTGGGCTGGAGCCACCTGACTCAGGTGGTTCTGCATCTGGGTGAAGAGGAAGTGGCCTGGACTGAGGAGGCCTTGGGGGAACGGTTTCTGCAAGCCCTGGAGTTTCTGGTGGGCAGCTTGGAGCAGGCTAGCCTGCCCTGTCACTTCAACCCCAGTGTGAACCTCTTGGGTAACTTCCGGGAAGAGGAGATTGATGACATTGGCTACGTGCTGTACAGCGGCCTCCAGGTTCCTGAAAGCCTATTCTAG",
      "ATGGCGGCCGCCAGCGGCTACACCGACCTGCGGGAGAAGCTCAAGTCCATGACGTCCCGGGACAACTACAAGGCGGGCAGTCGGGAGGCCGCCGCCGCTGCGGCCGCCGCCGTGGCTGCCGCTGCCGCTGCCGCGGCCGCCGCTGAGCCTTACCCGGCGTCCGGGACCACCAAGCGGAAATACCAGGAGGACTCGGACCCCGAGCGCAGCGACTACGAGGAGCATCAGTTGCAGAAGGAGGAAGAGGCGCGCAAGGTGAAGAGCGGCATCCGGCAGATCCGGCTCTTCAGTCAGGATGAGTGCTCCAAGATCGAGGCCCGCATCGATGAGGTGGTGTCCCGCGCCGAGAAGGGCCTGTACAACGAGCACACGGTGGACCGGGCCCCCCTGCGCAACAAGTACTTCTTCGGCGAGGGCTACACGTACGGGGCCCAGCTGCAGAAGCGCGGGCCGGGCCAGGAGCGCCTCTACCCGCCGGGCGACGTCGACGAGATCCCGGACTGGGTGCATCAGCTGGTGATCCAGAAGCTGGTGGAGCACCGCGTCATCCCCGAGGGCTTCGTCAACAGCGCGGTCATCAACGACTACCAGCCCGGCGGCTGCATCGTGTCCCACGTTGACCCCATCCACATCTTCGAGCGCCCCATCGTGTCCGTGTCTTTCTTCAGCGACTCGGCACTTTGCTTCGGCTGCAAGTTCCAGTTCAAGCCCATCCGGGTGTCGGAACCTGTGCTTTCTCTGCCGGTGCGCAGGGGGAGCGTGACTGTGCTCAGTGGGTATGCTGCTGATGAAATCACTCACTGCATACGGCCTCAGGACATTAAGGAACGCCGGGCGGTCATCATTCTCAGGAAGACAAGATTAGATGCACCGCGATTGGAAACAAAATCCCTGAGCAGCTCCACATTGCCACCCAGCTATGCTTCAGATCGCCTGTCAGGAAACACCAGAGACCCTGCGCTGAAACCCAAAAGGTCCCACCGCAAGGCAGACCCTGATGCTGCCCACAGGCCCCGGATCCTGGAAATGGACAAAGAAGAAAACCGGCGGTCTGTGCTCCTGCCCACACACCGGCGGAGGGGGAGTTTTAGCTCTGAGAACTATTGGCGCAAAGCCTATGAGTCCTCGGAAGATTGCCCAGAGGCAGCCAGCAGCCCCACCCGCAAGGTGAAGATGAGGAGACACTGA"
    )
  )
})