tests/testthat/test-mouse_orgAnn_annotateExon.R

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

test_that("test_mouse_orgAnn_annotateExon",  {
   inputFilePath = system.file("extdata", "RIPK1stop.fa", 
       package = "CRISPRseek")
## org.Dm.egFLYBASE2EG
## org.At.tair.db
## org.At.tairSYMBOL
## org.Ce.egSYMBOL
## org.Mm.egSYMBOL
## org.Rn.egSYMBOL
## org.Dr.egSYMBOL
## org.Hs.egSYMBOL

   test.gRNAPlusPAM <- TRUE

   outputDir <- getwd();
   REpatternFile <- system.file("extdata", "NEBenzymes.fa", package = "CRISPRseek")

   summary.NOorgAnn <- read.table(
       system.file("extdata/testMouse/NOorgAnn",
       "Summary.xls", package = "CRISPRseek"), sep = "\t", header = TRUE,
        stringsAsFactors = FALSE)
   offtarget.NOorgAnn  <- read.table(
       system.file("extdata/testMouse/NOorgAnn",
       "OfftargetAnalysis.xls", package = "CRISPRseek"), sep = "\t",
        header = TRUE, stringsAsFactors = FALSE)

   summary.WithorgAnn <- read.table(
	        system.file("extdata/testMouse/WithorgAnn",
	           "Summary.xls", package = "CRISPRseek"), sep = "\t", header = TRUE,
	        stringsAsFactors = FALSE)
   offtarget.WithorgAnn  <- read.table(
	     system.file("extdata/testMouse/WithorgAnn",
	          "OfftargetAnalysis.xls", package = "CRISPRseek"), sep = "\t",
	     header = TRUE, stringsAsFactors = FALSE)

   summary.NOTannotateExon <- read.table(
	     system.file("extdata/testMouse/NOTannotateExon",
 	         "Summary.xls", package = "CRISPRseek"), sep = "\t", header = TRUE,
	     stringsAsFactors = FALSE)
   offtarget.NOTannotateExon  <- read.table(
	     system.file("extdata/testMouse/NOTannotateExon",
	         "OfftargetAnalysis.xls", package = "CRISPRseek"), sep = "\t",
	      header = TRUE, stringsAsFactors = FALSE)

   summary.WithorgAnn <- summary.WithorgAnn[,1:21]
   summary.NOorgAnn <- summary.NOorgAnn [,1:21]
   summary.NOTannotateExon <- summary.NOTannotateExon[,1:21]

   if (!test.gRNAPlusPAM)
   {
     exclude.sum.col <-  grep("gRNAsPlusPAM", colnames(summary.WithorgAnn))
     exclude.oft.col <- grep("gRNAPlusPAM", colnames(offtarget.WithorgAnn)) 
     offtarget.NOTannotateExon <- offtarget.NOTannotateExon[, -exclude.oft.col]
     summary.NOTannotateExon <- summary.NOTannotateExon[, -exclude.sum.col]
     offtarget.WithorgAnn <- offtarget.WithorgAnn[, -exclude.oft.col]
     summary.WithorgAnn <- summary.WithorgAnn[, -exclude.sum.col]
     summary.NOorgAnn <- summary.NOorgAnn[, -exclude.sum.col]
     offtarget.NOorgAnn <- offtarget.NOorgAnn[, -exclude.oft.col]
   }
   chroms <- c("chr1", "chr5", "chr13")

   cat("Testing for mouse with orgAnn...\n")
   offTargetAnalysis(inputFilePath, findgRNAs = TRUE, 
	  findgRNAsWithREcutOnly = FALSE, findPairedgRNAOnly = FALSE,
	  BSgenomeName = Mmusculus, annotateExon=TRUE, 
          chromToSearch = chroms,
          min.score = 0.5, topN = 100, outputDir = outputDir, 
	  overwrite = TRUE, max.mismatch=1, txdb = TxDb.Mmusculus.UCSC.mm10.knownGene,
	  orgAnn = org.Mm.egSYMBOL)
	
    summary <- read.table("Summary.xls", sep = "\t", header = TRUE, 
        stringsAsFactors = FALSE)
    offtarget <- read.table("OfftargetAnalysis.xls", sep = "\t", header = TRUE, 
        stringsAsFactors = FALSE)
   if (!test.gRNAPlusPAM)
   {
       summary <- summary[, -exclude.sum.col]
       offtarget <- offtarget[, -exclude.oft.col]
   }
    expect_equal(summary.WithorgAnn, summary, tolerance = 0.01)
    expect_equal(offtarget.WithorgAnn, offtarget,tolerance = 0.001)

    cat("Testing for mouse without orgAnn...\n")

    expect_warning(offTargetAnalysis(inputFilePath, findgRNAs = TRUE, 
	        findgRNAsWithREcutOnly = FALSE, findPairedgRNAOnly = FALSE,
	        BSgenomeName = Mmusculus, annotateExon=TRUE, 
          chromToSearch = chroms,
          min.score = 0.5, topN = 100, outputDir = outputDir, 
	        overwrite = TRUE, max.mismatch=1, 
	        txdb = TxDb.Mmusculus.UCSC.mm10.knownGene))
	
    summary <- read.table("Summary.xls", sep = "\t", header = TRUE, 
		     stringsAsFactors = FALSE)
    offtarget <- read.table("OfftargetAnalysis.xls", sep = "\t", header = TRUE, 
		     stringsAsFactors = FALSE)
    if (!test.gRNAPlusPAM)
   {
       summary <- summary[, -exclude.sum.col]
       offtarget <- offtarget[, -exclude.oft.col]
   }
    expect_equal(summary.NOorgAnn, summary, tolerance = 0.01)
    expect_equal(offtarget.NOorgAnn, offtarget,tolerance = 0.001)
    cat("Testing for mouse without orgAnn...\n")
    offTargetAnalysis(inputFilePath, findgRNAs = TRUE, 
  	     findgRNAsWithREcutOnly = FALSE, findPairedgRNAOnly = FALSE,
         BSgenomeName = Mmusculus, annotateExon=FALSE, 
         chromToSearch = chroms,
         min.score = 0.5, topN = 100, outputDir = outputDir, 
	       overwrite = TRUE, max.mismatch=1)
	
    summary <- read.table("Summary.xls", sep = "\t", header = TRUE, 
	      stringsAsFactors = FALSE)
    offtarget <- read.table("OfftargetAnalysis.xls", sep = "\t", header = TRUE, 
	      stringsAsFactors = FALSE)
    if (!test.gRNAPlusPAM)
   {
       summary <- summary[, -exclude.sum.col]
       offtarget <- offtarget[, -exclude.oft.col]
   }
    expect_equal(summary.NOTannotateExon, summary, tolerance = 0.01)
    expect_equal(offtarget.NOTannotateExon, offtarget,tolerance = 0.001)
})