tests/testthat/test_AnnotationFilter.R

In Bioconductor/AnnotationFilter: Facilities for Filtering Bioconductor Annotation Resources

context("AnnotationFilter")

test_that("supportedFilters() works", {
    expect_true(inherits(supportedFilters(), "data.frame"))
    expect_identical(
        nrow(supportedFilters()),
        length(unlist(AnnotationFilter:::.FIELD, use.names=FALSE)) +
            length(AnnotationFilter:::.FILTERS_WO_FIELD)
    )
})

test_that("SymbolFilter as representative for character filters", {
    expect_true(validObject(new("SymbolFilter")))
    expect_error(SymbolFilter())
    expect_error(SymbolFilter(1, ">"))
    expect_error(SymbolFilter(1, "foo"))
    expect_error(SymbolFilter(c("foo","bar"), "startsWith"))
    ## Getter / setter
    fl <- SymbolFilter("BCL2")
    expect_equal(value(fl), "BCL2")
    fl <- SymbolFilter(c(4, 5))
    expect_equal(value(fl), c("4", "5"))
    fl <- SymbolFilter(3)
    expect_equal(value(fl), "3")
    expect_error(SymbolFilter(NA))
    ## condition.
    expect_equal(condition(fl), "==")
    fl <- SymbolFilter("a", condition = "!=")
    expect_equal(condition(fl), "!=")
    expect_error(SymbolFilter("a", condition = "<"))
    expect_error(SymbolFilter("a", condition = ""))
    expect_error(SymbolFilter("a", condition = c("==", ">")))
    expect_error(SymbolFilter("a", condition = NULL))
    expect_error(SymbolFilter("a", condition = NA))
    expect_error(SymbolFilter("a", condition = 4))
})

test_that("GeneStartFilter as representative for integer filters", {
    gsf <- GeneStartFilter(10000, condition = ">")
    expect_equal(condition(gsf), ">")
    expect_error(GeneStartFilter("3"))
    expect_error(GeneStartFilter("B"))
    expect_error(GeneStartFilter(NA))
    expect_error(GeneStartFilter(NULL))
    expect_error(GeneStartFilter())
    ## Condition
    expect_error(GeneStartFilter(10000, condition = "startsWith"))
    expect_error(GeneStartFilter(10000, condition = "endsWith"))
    expect_error(GeneStartFilter(10000, condition = c("==", "<")))
})

test_that("GRangesFilter works", {
    GRanges <- GenomicRanges::GRanges
    grf <- GRangesFilter(GRanges("chr10:87869000-87876000"))
    expect_equal(condition(grf), "any")
    expect_error(GRangesFilter(value = 3))
    expect_error(GRangesFilter(
        GRanges("chr10:87869000-87876000"),
        type = "=="
    ))
    grf <- GRangesFilter(
        GRanges("chr10:87869000-87876000"),
        type = "within",
        feature = "tx"
    )
    expect_equal(condition(grf), "within")
    expect_equal(feature(grf), "tx")
})

test_that("fieldToClass works", {
    expect_identical(AnnotationFilter:::.fieldToClass("gene_id"),
                     "GeneIdFilter")
    ## Support replacement for multiple _ : issue #13
    expect_identical(AnnotationFilter:::.fieldToClass("gene_seq_start"),
                     "GeneSeqStartFilter")
})

test_that("convertFilter Works", {
    expect_identical(convertFilter(SymbolFilter("ADA")), "symbol == 'ADA'")
    expect_identical(convertFilter(SymbolFilter("ADA", "!=")),
        "symbol != 'ADA'")
    expect_identical(convertFilter(SymbolFilter("ADA", "startsWith")),
        "symbol %like% 'ADA%'")
    expect_identical(convertFilter(SymbolFilter("ADA", "endsWith")),
        "symbol %like% '%ADA'")
    expect_identical(convertFilter(SymbolFilter("ADA", "contains")),
        "symbol %like% 'ADA'")
    
    expect_identical(convertFilter(TxStartFilter(1000)), "tx_start == '1000'")
    expect_identical(convertFilter(TxStartFilter(1000, "!=")),
        "tx_start != '1000'")
    expect_identical(convertFilter(TxStartFilter(1000, ">")), "tx_start > 1000")
    expect_identical(convertFilter(TxStartFilter(1000, "<")), "tx_start < 1000")
    expect_identical(convertFilter(TxStartFilter(1000, ">=")),
        "tx_start >= 1000")
    expect_identical(convertFilter(TxStartFilter(1000, "<=")),
        "tx_start <= 1000")

    ## check NOT works    

    expect_identical(convertFilter(SymbolFilter("ADA", not=TRUE)),
        "!symbol == 'ADA'")
    expect_identical(convertFilter(SymbolFilter("ADA", "!=", not=TRUE)),
        "!symbol != 'ADA'")
    expect_identical(convertFilter(SymbolFilter("ADA", "startsWith", not=TRUE)),
        "!symbol %like% 'ADA%'")
    expect_identical(convertFilter(SymbolFilter("ADA", "endsWith", not=TRUE)),
        "!symbol %like% '%ADA'")
    expect_identical(convertFilter(SymbolFilter("ADA", "contains", not=TRUE)),
        "!symbol %like% 'ADA'")
    
    expect_identical(convertFilter(TxStartFilter(1000, not=TRUE)),
        "!tx_start == '1000'")
    expect_identical(convertFilter(TxStartFilter(1000, "!=", not=TRUE)),
        "!tx_start != '1000'")
    expect_identical(convertFilter(TxStartFilter(1000, ">", not=TRUE)),
        "!tx_start > 1000")
    expect_identical(convertFilter(TxStartFilter(1000, "<", not=TRUE)),
        "!tx_start < 1000")
    expect_identical(convertFilter(TxStartFilter(1000, ">=", not=TRUE)),
        "!tx_start >= 1000")
    expect_identical(convertFilter(TxStartFilter(1000, "<=", not=TRUE)),
        "!tx_start <= 1000")
})