tests/testthat/test_tirClust.R

In packFinder: de novo Annotation of Pack-TYPE Transposable Elements

context("clustering functions")

dir.create("tempTestOutput")
data("arabidopsisThalianaRefseq")
data("packMatches")
load("data-r/consensusSeqs.rda")

consensusSeqTest <- tirClust(packMatches,
    arabidopsisThalianaRefseq,
    tirLength = 25,
    plot = FALSE
)

test_that("no errors thrown by tirClust", {
    expect_silent(tirClust(packMatches,
        arabidopsisThalianaRefseq,
        tirLength = 25,
        plot = FALSE,
        plotSavePath = "tempTestOutput/tirRelationships.png"
    ))
})

test_that("consensus sequences returned are as expected", {
    expect_equal(as.character(consensusSeqTest), as.character(consensusSeqs))
})

unlink("tempTestOutput", recursive = TRUE)