tests/testthat/test.removeEmptySeqs.R

In fmichonneau/chopper: Alignment Manipulations and Data Preparation for Phylogenetic Analyses

context("removeEmptySeqs")

test_that("phylip gaps as -", {
    cat("3 6",
        "sp1   at-t-t",
        "sp2   gt----",
        "sp3   ------",
        sep="\n", file="testPhy.phy")
    resMade <- removeEmptySeqs("testPhy.phy", output="testPhy_red.phy",
                               formatin="sequential")
    resOut <- ape::read.dna(file="testPhy_red.phy", format="sequential")
    expect_equal(dim(resOut), c(2, 6))
    expect_equal(dimnames(resOut)[[1]], c("sp1", "sp2"))
    expect_error(
        resMade <- removeEmptySeqs("testPhy.phy", formatin="seq",
                                   overwrite=FALSE)
        )
    resMade <- removeEmptySeqs("testPhy.phy", formatin="seq",
                               overwrite=TRUE)
    expect_equal(resMade, "sp3")
    unlink("testPhy.phy")
    unlink("testPhy_red.phy")
})

test_that("phylip gaps as *", {
    cat("3 6",
        "sp1   at-t-t",
        "sp2   gt----",
        "sp3   ******",
        sep="\n", file="testPhy.phy")
    resMade <- removeEmptySeqs("testPhy.phy", output="testPhy_red.phy",
                               formatin="sequential")
    resOut <- ape::read.dna(file="testPhy_red.phy", format="sequential")
    expect_equal(dim(resOut), c(2, 6))
    expect_equal(dimnames(resOut)[[1]], c("sp1", "sp2"))
    expect_error(
        resMade <- removeEmptySeqs("testPhy.phy", formatin="seq",
                                   overwrite=FALSE)
        )
    resMade <- removeEmptySeqs("testPhy.phy", formatin="seq",
                               overwrite=TRUE)
    expect_equal(resMade, "sp3")
    unlink("testPhy.phy")
    unlink("testPhy_red.phy")
})

test_that("a sequence with only a letter is not considered a gap", {
    cat("3 6",
        "sp1 aaaaaa",
        "sp2 ----tt",
        "sp3 ------",
        sep = "\n", file = "testPhy.phy")
    resMade <- removeEmptySeqs("testPhy.phy", output = "testPhy_red.phy",
                               formatin = "sequential")
    resOut <- ape::read.dna(file = "testPhy_red.phy", format = "sequential")
    expect_equal(dim(resOut), c(2, 6))
    expect_equal(dimnames(resOut)[[1]], c("sp1", "sp2"))
    unlink("testPhy.out")
    unlink("testPhy_red.out")
})