tests/testthat/test-deepCpf1.R

In LihuaJulieZhu/CRISPRseek: Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

test_need_tensorflow <- function() {
  test_that(
     "extendedSequence is required for DeepCpf1 algorithm", {
        expect_error(deepCpf1())
  })

  test_that(
     "deepcpf1 expects the sequence to be 34 base long", {
        expect_warning(deepCpf1("AATGAAA"))
  })

  test_that("test_deepCpf1", {
      extendedSequence = c("GTTATTTGAGCAATGCCACTTAATAAACATGTAA",
          "TGACTTTGAATGGAGTCGTGAGCGCAAGAACGCT", "GTTATTTGAGCAATGCCACTTAATAAACATGTAA",
          "TGACTTTGAATGGAGTCGTGAGCGCAAGAACGCT")
      chrom_acc = c(0, 1, 1, 0)
      seq.DeepScore = c(53.46983, 55.69931, 53.46983, 55.69931)/100
      DeepScore = c(7.932924, 46.077484, 44.095499, 8.181222)/100
      effi_noacc <- deepCpf1(extendedSequence)
      effi_acc <- deepCpf1(extendedSequence, chrom_acc)
      expect_equal(DeepScore, effi_acc, tolerance = 0.001)
      expect_equal(seq.DeepScore, effi_noacc, tolerance = 0.001)
      extendedSequence <- readRDS(system.file("extdata/all.gRNAs.df.RDS",
          package = "CRISPRseek"))
      extendedSequence <- extendedSequence[, 5]
      chrom_acc <- rep(c(0, 1), 10)
      effi_noacc2 <- deepCpf1(extendedSequence)
      effi_acc2 <- deepCpf1(extendedSequence, chrom_acc)
      seq.DeepScore2 <- deepCpf1(extendedSequence[-c(1, 2)])
      DeepScore2 <- deepCpf1(extendedSequence[-c(1, 2)], chrom_acc[-c(1,
          2)])
      expect_equal(DeepScore2, effi_acc2[-c(1, 2)], tolerance = 0.001)
      expect_equal(seq.DeepScore2, effi_noacc2[-c(1, 2)], tolerance = 0.001)
      expect_equal(c(NA, NA, 0.01009442), deepCpf1(extendedSequence[1:3]), tolerance = 0.001)
      expect_equal(0.0100944, deepCpf1(extendedSequence[3]), tolerance = 0.0001)
      suppressWarnings(expect_equal(deepCpf1(extendedSequence[1]),
          NA))
  })

  test_that("test_deepCpf1BaseMissing", {
      extendedSequence = c("GTTATTTGAGCAATGCCACTTAATAAACATGTAA",
          "TGACTTTGAATGGAGTCGTGAGCGCAAGAACGCT", "GTTATTTGAGCAATGCCACTTAATAAACATGTAA",
          "TGACTTTGAATGGAGTCGTGAGCGCAAGAACGCT")
      new.seq <- c(extendedSequence, "GTAGTTTTGAGAGATTTTATTGGTATTGATTTGT")
      eff <- deepCpf1(new.seq)
      seq.DeepScore = c(53.46983, 55.69931, 53.46983, 55.69931)/100
      expect_equal(seq.DeepScore, eff[1:4], tolerance = 0.001)
      extendedSeq <- readRDS(system.file("extdata/testSeqForDeepCpf1.RDS",
          package = "CRISPRseek"))
      eff.40 <- deepCpf1(extendedSeq[1:40])
      eff <- deepCpf1(extendedSeq)
      expect_equal(eff[1:40], eff.40, tolerance = 0.001)
  })

  test_that("test_gRNAInGenomeCpf1", {
      results2 <- offTargetAnalysis(inputFilePath = system.file("extdata",
          "cpf1-2.fa", package = "CRISPRseek"), findgRNAsWithREcutOnly = FALSE,
          findPairedgRNAOnly = FALSE, annotatePaired = FALSE, BSgenomeName = Hsapiens,
          chromToSearch = "chr8", txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
          orgAnn = org.Hs.egSYMBOL, max.mismatch = 1, baseBeforegRNA = 8,
          baseAfterPAM = 26, rule.set = "DeepCpf1", overlap.gRNA.positions = c(19,
              23), useEfficacyFromInputSeq = FALSE, outputDir = getwd(),
          overwrite = TRUE, PAM.location = "5prime", PAM.size = 4,
          PAM = "TTTN", PAM.pattern = "^TNNN", allowed.mismatch.PAM = 2,
          subPAM.position = c(1, 2))
      effi_truth <- deepCpf1(results2$summary[!is.na(results2$summary[,
          2]), 3])
      expect_equal(effi_truth, as.numeric(results2$summary[!is.na(results2$summary[,
          2]), 4]), tolerance = 0.001)
      effi_truth <- deepCpf1(results2$offtarget$extendedSequence)
      expect_equal(effi_truth, results2$offtarget$gRNAefficacy, tolerance = 0.001)
  })

  test_that("test_gRNAWithOffCpf1", {
      results3 <- offTargetAnalysis(inputFilePath = system.file("extdata",
          "cpf1-2.fa", package = "CRISPRseek"), findgRNAsWithREcutOnly = FALSE,
          findPairedgRNAOnly = FALSE, annotatePaired = FALSE, BSgenomeName = Hsapiens,
          chromToSearch = paste0("chr", 1:21), txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
          orgAnn = org.Hs.egSYMBOL, max.mismatch = 3, baseBeforegRNA = 8,
          baseAfterPAM = 26, rule.set = "DeepCpf1", overlap.gRNA.positions = c(19,
              23), useEfficacyFromInputSeq = FALSE, outputDir = getwd(),
          overwrite = TRUE, PAM.location = "5prime", PAM.size = 4,
          PAM = "TTTN", PAM.pattern = "^TNNN", allowed.mismatch.PAM = 2,
          subPAM.position = c(1, 2))
      effi_truth <- deepCpf1(results3$summary[!is.na(results3$summary[,
          2]), 3])
      expect_equal(effi_truth, as.numeric(results3$summary[!is.na(results3$summary[,
          2]), 4]), tolerance = 0.001)
      effi_truth <- deepCpf1(results3$offtarget$extendedSequence)
      expect_equal(effi_truth, results3$offtarget$gRNAefficacy, tolerance = 0.001)
  })

  test_that("test_somegRNAsNotInGenomeCpf1", {
      gRNAs_truth <- readRDS(system.file("extdata", "gRNAsCpf1.RDS",
          package = "CRISPRseek"))
      results1 <- offTargetAnalysis(inputFilePath = gRNAs_truth,
          findgRNAs = FALSE, gRNAoutputName = "testCpf1gRNA.fa",
          annotatePaired = FALSE, BSgenomeName = Hsapiens, chromToSearch = "chrX",
          txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, orgAnn = org.Hs.egSYMBOL,
          max.mismatch = 0, baseBeforegRNA = 8, baseAfterPAM = 26,
          rule.set = "DeepCpf1", PAM.size = 4, gRNA.size = 20,
          overlap.gRNA.positions = c(19, 23), outputDir = getwd(),
          overwrite = TRUE, PAM.location = "5prime", PAM = "TTTN",
          PAM.pattern = "^TNNN", allowed.mismatch.PAM = 2, subPAM.position = c(1,
              2))
      effi_truth <- deepCpf1(results1$summary[!is.na(results1$summary[,
          2]), 3])
      expect_equal(effi_truth, as.numeric(results1$summary[!is.na(results1$summary[,
          2]), 4]), tolerance = 0.001)
      effi_truth <- deepCpf1(results1$offtarget$extendedSequence)
      expect_equal(effi_truth, results1$offtarget$gRNAefficacy, tolerance = 0.001)
  })
}

# test_need_tensorflow()