tests/testthat/test_getSeqsAcrossBSJs.R

In circRNAprofiler: circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

setwd(file.path(getwd(), "testdata"))

context("Test that getSeqsAcrossBSJs() function works correctly")
test_that("getSeqsAcrossBSJs() retrieves the correct sequences", {
    gtf <- formatGTF(pathToGTF = "gencodeVM16.gtf")

    # Create the backSplicedJunctions data frame
    backSplicedJunctions <- getBackSplicedJunctions(gtf)
    mergedBSJunctions <- mergeBSJunctions(backSplicedJunctions, gtf)
    # Retrive the genomic features
    annotatedBSJs <- annotateBSJs(mergedBSJunctions, gtf)

    if (requireNamespace("BSgenome.Mmusculus.UCSC.mm10", quietly = TRUE)){
        # Get BSgenome object
        genome <- BSgenome::getBSgenome("BSgenome.Mmusculus.UCSC.mm10")
        
        # retrieve target sequences
        targets <- getSeqsAcrossBSJs(annotatedBSJs,
                                     gtf,
                                     genome)
        
        # For positive strand
        expect_equal(targets$bsj$id[11], "Arhgap5:+:chr12:52516079:52542636")
        expect_equal(targets$bsj$length[11], 22)
        
        # The back-spliced sequences should be the one reported below
        expect_equal(targets$bsj$seq[11],  "UGAAGACACAGAGGAAGAUGAU")
        
        #For negative strand
        expect_equal(targets$bsj$id[7], "Eps15l1:-:chr8:72380306:72367904")
        expect_equal(targets$bsj$length[7], 22)
        
        # The back-spliced sequences should be the one reported below
        expect_equal(targets$bsj$seq[7], "AGAUGUCCAAGAUCUCAUCAUU") 
    }else{
        cat(
            "Missing package BSgenome.Mmusculus.UCSC.mm10.
            Use BiocManager to install it."
        )
    }


})