tests/testthat/test-compare2Sequences.R

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

test_that("test_compare2Sequences", {
    cat("testing compare2Sequences \n")
    inputFile1Path <- system.file("extdata", "rs362331T.fa",
    package = "CRISPRseek")
    inputFile2Path <- system.file("extdata", "rs362331C.fa",
    package = "CRISPRseek")
    dev.mode <- 0
   if (dev.mode == 1)
  {
    seqs1CFD <- compare2Sequences.bk(inputFile1Path, inputFile2Path,
        outputDir = getwd(), 
        overwrite = TRUE,scoring.method = "CFDscore")

    seqs1 <- compare2Sequences.bk(inputFile1Path, inputFile2Path,
        outputDir = getwd(), 
        overwrite = TRUE)

    seqs3CFD <- compare2Sequences3(inputFile1Path, inputFile2Path,
        outputDir = getwd(), 
        overwrite = TRUE,scoring.method = "CFDscore")

    seqs3 <- compare2Sequences3(inputFile1Path, inputFile2Path,
        outputDir = getwd(), 
        overwrite = TRUE)

   seqs1.5prime <- compare2Sequences.bk(inputFile1Path, inputFile2Path,
        outputDir = getwd(), PAM.location = "5prime", PAM = "GCT", PAM.pattern = "^NCN",
        overwrite = TRUE, subPAM.position = c(1,2))

   seqs3.5prime<- compare2Sequences3(inputFile1Path, inputFile2Path,
        outputDir = getwd(), PAM.location = "5prime", 
        PAM = "GCT", PAM.pattern = "^NCN",
        overwrite = TRUE, subPAM.position = c(1,2))
 }
   seqs2CFD.new <- compare2Sequences(inputFile1Path, inputFile2Path,
        outputDir = getwd(), 
        overwrite = TRUE,scoring.method = "CFDscore")

   seqs2.new <- compare2Sequences(inputFile1Path, inputFile2Path,
        outputDir = getwd(), 
        overwrite = TRUE)

   seqs2.5prime.new <- compare2Sequences(inputFile1Path, inputFile2Path,
        outputDir = getwd(), 
        PAM.location = "5prime", PAM = "GCT", PAM.pattern = "^NCN",
        overwrite = TRUE, subPAM.position = c(1,2))

#saveRDS(seqs2.5prime.new, file ="~/seqs2.5prime.RDS")
#saveRDS(seqs2.new, file = "~/seqs2..RDS")
#saveRDS(seqs2CFD.new, file = "~/seqs2CFD.RDS")

     seqs2 <- readRDS(system.file("extdata", "seqs2.RDS", 
          package = "CRISPRseek"))
     seqs2CFD <- readRDS(system.file("extdata", "seqs2CFD.RDS", 
          package = "CRISPRseek"))
    seqs2.5prime <- readRDS(system.file("extdata", "seqs2.5prime.RDS",
          package = "CRISPRseek"))
    expect_equal(seqs2[, -6], seqs2.new[, -6], tolerance = 0.001)
    expect_equal(seqs2CFD[, -6], seqs2CFD.new[, -6], tolerance = 0.001)
    expect_equal(seqs2.5prime[, -6], seqs2.5prime.new[, -6], tolerance = 0.001)
    if (dev.mode == 1) {
        if (expect_equal(seqs2, seqs3)) {
            1
        }
        if (expect_equal(seqs2CFD, seqs3CFD)) {
            1
        }
        if (expect_equal(seqs2[, -c(2:4)], seqs1[, -c(2:4)])) {
            1
        }
        if (expect_equal(seqs2CFD[, -c(2:4)], seqs1CFD[, -c(2:4)])) {
            1
        }
        if (expect_equal(seqs3[, -c(2:4)], seqs1[, -c(2:4)])) {
            1
        }
        if (expect_equal(seqs3CFD[, -c(2:4)], seqs1CFD[, -c(2:4)])) {
            1
        }
        if (expect_equal(seqs2.5prime, seqs3.5prime)) {
            1
        }
        if (expect_equal(seqs3.5prime[, -c(2:4)], seqs1.5prime[, 
            -c(2:4)])) {
            1
        }
    }
})