inst/unitTests/test_get_ssRleCov.R

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

test_get_ssRleCov <- function() {
  ## generate a bedgraph file
  start <- seq(1, 9, by = 2)
  end <- seq(2, 10, by = 2)
  testGR <- GRanges("chr1", IRanges(start, end),
    strand = "+", score = 1:5
  )
  filename <- tempfile()
  export(testGR, filename, format = "BEDGraph")

  tag <- c("test")
  metadata <- data.frame(
    tag = tag,
    condition = "test",
    bedgraph_file = filename
  )
  outdir <- tempdir()
  write.table(metadata,
    file = file.path(outdir, "metadata.txt"),
    sep = "\t", quote = FALSE, row.names = FALSE
  )

  sqlite_db <- setup_sqlitedb(
    metadata = file.path(outdir, "metadata.txt"),
    outdir
  )
  addLockName(filename = tempfile())

  cov <- get_ssRleCov(
    bedgraph = filename,
    tag = "test",
    genome = BSgenome.Mmusculus.UCSC.mm10,
    sqlite_db = sqlite_db,
    outdir = outdir,
    chr2exclude = NULL
  )
  cov <- readRDS(cov$coverage_file[cov$tag == "test" & cov$chr == "chr1"])
  checkEquals(rep(2, 5), runLength(cov)[1:5])
  checkEquals(1:5, runValue(cov)[1:5])
}