tests/testthat/test-OtherMasking.R

In Bioconductor/Biostrings: Efficient manipulation of biological strings

## Additional tests for the following files:
## - maskMotif.R (contains `maskMotif`, `mask`)
## - injectHardMask.R (contains `injectHardMask`)

test_that("maskMotif works for XStrings", {
    s1 <- BString("aabbaacc")
    s2 <- maskMotif(s1, "bb")
    expect_equal(as.character(s2), "aa##aacc")
    s3 <- maskMotif(s2, "baac")
    expect_equal(as.character(s3), "aa##aacc")

    ## order of operations matters, masking should skip masked positions
    s4 <- maskMotif(s1, "baac")
    expect_equal(as.character(s4), "aab####c")
    expect_equal(as.character(gaps(s4)), "###baac#")
    expect_equal(as.character(as(s4, "Views")), c("aab", "c"))

    ## mask DNAString by multiple motifs
    ## example from ?maskMotif.R, just using DNAString objects
    x <- DNAString("ACACAACTAGATAGNACTNNGAGAGACGC")
    x1 <- maskMotif(x, DNAString("N"))
    x2 <- maskMotif(x1, DNAString("AC"))
    x3 <- maskMotif(x2, DNAString("GA"), min.block.width=5)
    expect_equal(width(as(x3, "Views")), c(1,7,1,5,2))
    exp_opt <- c(A=5L, C=5L, N=3L, `#`=16L)
    expect_true(all(table(strsplit(as.character(gaps(x3)), "")[[1]]) ==
                    as.table(exp_opt[order(names(exp_opt))])))
})

test_that("injectHardMask works for all supported inputs", {
    set.seed(50L)
    ds <- sample(DNA_BASES, 50L, replace=TRUE)

    d1 <- DNAString(paste(ds, collapse=""))
    d2 <- d1

    mask_starts <- c(4,10,28)
    mask_ends <- c(7,17,38)
    m1 <- Mask(length(ds), start=mask_starts, end=mask_ends)
    masks(d2) <- m1

    all_masked_indices <- unlist(
        lapply(seq_along(mask_starts),
               function(i) seq(mask_starts[i], mask_ends[i]))
    )
    exp_opt <- ds
    exp_opt[all_masked_indices] <- "+"
    expect_equal(as.character(injectHardMask(d2)),
                 paste(exp_opt, collapse=""))

    exp_opt[all_masked_indices] <- "M"
    expect_equal(as.character(injectHardMask(d2, "M")),
                 paste(exp_opt, collapse=""))

    v <- Views(d1, start=mask_starts, end=mask_ends)
    ## injecting on a Views does the opposite
    all_vmasked <- seq_len(length(ds))[-all_masked_indices]
    exp_vopt <- ds
    exp_vopt[all_vmasked] <- "+"
    expect_equal(as.character(injectHardMask(v)),
                 paste(exp_vopt, collapse=""))

    exp_vopt[all_vmasked] <- "M"
    expect_equal(as.character(injectHardMask(v, "M")),
                 paste(exp_vopt, collapse=""))
})