tests/testthat/test_ExtendSeqContextForOnebpINDEL.R

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

test_that("ExtendSeqContextForOnebpINDEL", {
  # Please see "./data-raw/code/create_testdata_for_ID_extended_sequences.R"
  # for generating the test data

  load("testdata/test_ExtendSeqContextForOnebpINDEL.Rdata")

  test.INS.T.1.0.sequences <-
    SymmetricalContextsFor1BPIndel(test.indel.vcf, indel.class = "INS:T:1:0",
                                   flank.length = 10)
  test.INS.T.1.4.sequences <-
    SymmetricalContextsFor1BPIndel(test.indel.vcf, indel.class = "INS:T:1:4",
                                   flank.length = 6)
  test.DEL.C.1.0.sequences <-
    SymmetricalContextsFor1BPIndel(test.indel.vcf, indel.class = "DEL:C:1:0",
                                   flank.length = 10)
  test.DEL.C.1.4.sequences <-
    SymmetricalContextsFor1BPIndel(test.indel.vcf, indel.class = "DEL:C:1:4",
                                   flank.length = 6)

  expect_equal(test.INS.T.1.0.sequences, INS.T.1.0.sequences)
  expect_equal(test.INS.T.1.4.sequences, INS.T.1.4.sequences)
  expect_equal(test.DEL.C.1.0.sequences, DEL.C.1.0.sequences)
  expect_equal(test.DEL.C.1.4.sequences, DEL.C.1.4.sequences)
})

test_that("errors", {
  expect_error(
    Get1BPIndelFlanks(sequence = "CTCTTTGTGAAGTAGCAACAGTTACATTTAAAATTTAAAACAC",
                      ref = "T",  alt = "TT",  indel.class = "INS:T:1:2"))
# [1] "ACAGTTACATTT"
  expect_error(
    Get1BPIndelFlanks(sequence = "ATATAATTTGAATAAAAAGGTTTTGGAATACTGAAAAGTCTCC",
                      ref = "T",  alt = "TT",  indel.class = "INS:T:1:4"))
# [1] "AGGTTTTGGAATAC"
  expect_error(
    Get1BPIndelFlanks(sequence = "CTGGCTAATTTTTTGTATTGTTTTTAGTAGAGACGGGGGTTTGC",
                      ref = "TT",  alt = "T",  indel.class = "DEL:T:1:4"))
# [1] "TTGTTTTTAGTAGAG"
})