tests/testthat/test-findgRNAs.R

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

library(CRISPRseek)
test_need_tensorflow <- function() {
  test_that("test_findgRNAsCpf1", {
      gRNAs <- findgRNAs(inputFilePath = system.file("extdata",
          "cpf1.fa", package = "CRISPRseek"), findPairedgRNAOnly = FALSE,
          pairOutputFile = "testpairedgRNAs-cpf1.xls", PAM = "TTTN",
          PAM.location = "5prime", PAM.size = 4, overlap.gRNA.positions = c(19,
              23), baseBeforegRNA = 8, baseAfterPAM = 26, calculategRNAEfficacy = TRUE,
          rule.set = "DeepCpf1", efficacyFile = "testcpf1Efficacy.xls")
      gRNAs_truth <- readRDS(system.file("extdata", "gRNAsCpf1.RDS",
          package = "CRISPRseek"))
      expect_equal(as.character(gRNAs), as.character(gRNAs_truth))
      effi_truth <- readRDS(system.file("extdata", "Cpf1Eff.RDS",
          package = "CRISPRseek"))
      effi <- read.table("testcpf1Efficacy.xls", sep = "\t", header = TRUE)
      expect_equal(effi_truth, effi, tolerance = 0.001)
  })
}

# test_need_tensorflow()

test_that("test_findgRNAsSpCas9", {
    featureWeightMatrixFile <- system.file("extdata", "Morenos-Mateo.csv",
        package = "CRISPRseek")
    gRNAs <- findgRNAs(inputFilePath = system.file("extdata",
        "cpf1.fa", package = "CRISPRseek"), findPairedgRNAOnly = FALSE,
        pairOutputFile = "testpairedgRNAs-SpCas9.xls", PAM = "NGG",
        PAM.location = "3prime", PAM.size = 3, overlap.gRNA.positions = c(17,
            18), baseBeforegRNA = 4, baseAfterPAM = 3, calculategRNAEfficacy = TRUE,
        rule.set = "CRISPRscan", featureWeightMatrixFile = featureWeightMatrixFile,
        efficacyFile = "testCRISPRscanEfficacy.xls")
    gRNAs_truth <- readRDS(system.file("extdata", "gRNAsSpCas9.RDS",
        package = "CRISPRseek"))
    expect_equal(as.character(gRNAs_truth),as.character(gRNAs))
    effi_truth <- readRDS(system.file("extdata", "CRISPRscanEff.RDS",
        package = "CRISPRseek"))
    effi <- read.table("testCRISPRscanEfficacy.xls", sep = "\t",
        header = TRUE)
    expect_equal(effi_truth, effi, tolerance = 0.001)
})