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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")
})
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