tests/testthat/test-fimo.R

In snystrom/memes: motif matching, comparison, and de novo discovery using the MEME Suite

skip_if_not(meme_is_installed())

test_that("runFimo works", {
  peaks <- system.file(
    "extdata/peaks/peaks.tsv",
    package = "memes",
    mustWork = TRUE
  ) %>%
    readr::read_tsv(
      col_types = c("seqnames" = "c", "start" = "i", "end" = "i")
    ) %>%
    GenomicRanges::GRanges()

  dm.genome <- BSgenome.Dmelanogaster.UCSC.dm6::BSgenome.Dmelanogaster.UCSC.dm6

  e93_motif <- universalmotif::create_motif(
    "CCRAAAW",
    name = "E93",
    altname = "Eip93F"
  )

  regions <- peaks %>%
    GenomicRanges::resize(200, fix = "center")

  fimo_res <- regions %>%
    get_sequence(dm.genome) %>%
    runFimo(e93_motif, thresh = 1e-3, skip_matched_sequence = FALSE) %>%
    add_sequence(dm.genome)

  expect_s4_class(fimo_res, "GenomicRanges")

  # Ensure add_sequence matches the detected sequences
  fimo_res %<>% add_sequence(dm.genome)
  expect_equal(fimo_res$matched_sequence, fimo_res$sequence)

  # errror no names in header
  seq <- universalmotif::create_sequences()
  motif <- universalmotif::create_motif()
  expect_message(
    try(runFimo(seq, motif, parse_genomic_coord = FALSE), silent = TRUE),
    "header"
  )
  expect_error(suppressMessages(runFimo(
    seq,
    motif,
    parse_genomic_coord = FALSE
  )))

  # run, but message "no matches detected"
  names(seq) <- seq_along(seq)
  expect_null(suppressMessages(runFimo(seq, motif, thresh = 1e-10)))
  expect_message(
    runFimo(seq, motif, thresh = 1e-10),
    "No matches were detected"
  )

  # run, but message "no matches detected" if text = FALSE
  expect_null(suppressMessages(runFimo(
    seq,
    motif,
    thresh = 1e-10,
    text = FALSE
  )))
  expect_message(
    runFimo(seq, motif, thresh = 1e-10, text = FALSE),
    "No matches were detected"
  )

  # Suggest psp instead of psspp
  expect_error(
    suppressMessages(runFimo(seq, motif, psspp = 'x')),
    class = "usethis_error",
    regexp = "Invalid flags"
  )
  expect_message(
    try(runFimo(seq, motif, psspp = 'x'), silent = TRUE),
    "Error processing command line options"
  )
})

test_that("import works", {
  expect_error(importFimo("/file/does/not/exist"))
  expect_error(parseFimo("/file/does/not/exist"))
  expect_s4_class(
    importFimo(system.file(
      "extdata/fimo.tsv",
      package = "memes",
      mustWork = TRUE
    )),
    "GRanges"
  )
})