tests/testthat/test_convert.R

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

context("convert")

dir.create("tempTestOutput")
data("arabidopsisThalianaRefseq")
print(arabidopsisThalianaRefseq)
data("packMatches")

packsToCsv(packMatches, file = "tempTestOutput/packMatches.csv")

packsToFasta(packMatches = packMatches, 
            file = "tempTestOutput/packMatches.fasta", 
            Genome = arabidopsisThalianaRefseq)

packsGRanges <- packsToGRanges(packMatches)

packsFromCsv <- getPacksFromCsv(file = "tempTestOutput/packMatches.csv")
packsFromFasta <- getPacksFromFasta("tempTestOutput/packMatches.fasta")
packsFromGRanges <- getPacksFromGRanges(packsGRanges)

# ignore differences in column type
packsFromCsv$seqnames <- as.factor(packsFromCsv$seqnames)
packsFromFasta$seqnames <- as.factor(packsFromFasta$seqnames)
packsFromFasta$start <- as.integer(packsFromFasta$start)
packsFromFasta$end <- as.integer(packsFromFasta$end)
packsFromFasta$width <- as.integer(packsFromFasta$width)
packsFromGRanges$strand <- as.character(packsFromGRanges$strand)

test_that("Conversion functions create correct output from sample data", {
    expect_equal(as.character(packsFromCsv), as.character(packMatches))
    expect_equal(packsFromFasta, subset(packMatches, select = -c(cluster)))
    expect_equal(packsFromGRanges, packMatches)
})

unlink("tempTestOutput", recursive = TRUE)