tests/testthat/test-NxtIRFcore.R

In alexchwong/NxtIRFcore: Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

test_that("NxtIRF pipeline reproduces NxtSE object", {
    bams = NxtIRF_example_bams()
    chr_alias = data.frame(old = "chrZ", new = "chrZ")

    BuildReference(
        fasta = chrZ_genome(), 
        gtf = chrZ_gtf(),
        reference_path = file.path(tempdir(), "Reference"),
        chromosome_aliases = chr_alias
    )
    
    IRFinder(bams$path, bams$sample,
        reference_path = file.path(tempdir(), "Reference"),
        output_path = file.path(tempdir(), "IRFinder_output"),
        n_threads = 1
    )
    expr <- Find_IRFinder_Output(file.path(tempdir(), "IRFinder_output"))
    
    CollateData(expr, 
        reference_path = file.path(tempdir(), "Reference"),
        output_path = file.path(tempdir(), "NxtIRF_output")
    )

    se <- MakeSE(collate_path = file.path(tempdir(), "NxtIRF_output"))
    
    # Test identical assays
    se_realized = realize_NxtSE(se)
    
    se_compare <- NxtIRF_example_NxtSE()
    
    expect_equal(
        assay(se_realized, "Included"), 
        assay(se_compare, "Included")
    )

    expect_equal(
        assay(se_realized, "Excluded"), 
        assay(se_compare, "Excluded")
    )

    expect_equal(
        assay(se_realized, "minDepth"), 
        assay(se_compare, "minDepth")
    )

    expect_equal(
        assay(se_realized, "Depth"), 
        assay(se_compare, "Depth")
    )

    expect_equal(
        assay(se_realized, "Coverage"), 
        assay(se_compare, "Coverage")
    )

    expect_equal(
        sampleQC(se_realized)[,-1], 
        sampleQC(se_compare)[,-1]
    )

    for(i in seq_len(ncol(se))) {
        expect_equal(
            openssl::md5(file(covfile(se_realized)[i])), 
            openssl::md5(file(covfile(se_compare)[i]))
        )
    }

    expect_equal(
        up_inc(se_realized), 
        up_inc(se_compare)
    )

    expect_equal(
        up_exc(se_realized), 
        up_exc(se_compare)
    )

    expect_equal(
        down_inc(se_realized), 
        down_inc(se_compare)
    )

    expect_equal(
        down_exc(se_realized), 
        down_exc(se_compare)
    )

})