R/04.get_chromosomes.R

In haibol2016/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

#' Identify chromosomes/scaffolds for CP site discovery
#'
#' Identify chromosomes/scaffolds which have both coverage and annotated
#' 3' utr3 for CP site discovery
#'
#' @param utr3 An object of [GenomicRanges::GRangesList-class]. An output of
#'   [extract_UTR3Anno()].
#' @param sqlite_db A path to the SQLite database for InPAS, i.e. the output of
#'   [setup_sqlitedb()].
#'
#' @return A vector of characters, containing names of chromosomes/scaffolds
#'   for CP site discovery
#' @export
#' @examples
#' library(BSgenome.Mmusculus.UCSC.mm10)
#' genome <- BSgenome.Mmusculus.UCSC.mm10
#' data(utr3.mm10)
#' utr3 <- split(utr3.mm10, seqnames(utr3.mm10), drop = TRUE)
#' bedgraphs <- system.file("extdata", c(
#'   "Baf3.extract.bedgraph",
#'   "UM15.extract.bedgraph"
#' ),
#' package = "InPAS"
#' )
#' tags <- c("Baf3", "UM15")
#' metadata <- data.frame(
#'   tag = tags,
#'   condition = c("Baf3", "UM15"),
#'   bedgraph_file = bedgraphs
#' )
#' 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())
#' coverage <- list()
#' for (i in seq_along(bedgraphs)) {
#'       coverage[[tags[i]]] <- get_ssRleCov(
#'       bedgraph = bedgraphs[i],
#'       tag = tags[i],
#'       genome = genome,
#'       sqlite_db = sqlite_db,
#'       outdir = outdir,
#'       chr2exclude = "chrM"
#'     )
#' }
#' get_chromosomes(utr3, sqlite_db)
get_chromosomes <- function(utr3, sqlite_db) {
  if (missing(utr3) || !is(utr3, "GRangesList")) {
    stop("utr3 must be a GRangesList object")
  }
  if (missing(sqlite_db) || !file.exists(sqlite_db)) {
    stop("sqlite_db must be an exisiting path to SQLite database")
  }

  db_conn <- dbConnect(drv = RSQLite::SQLite(), dbname = sqlite_db)
  covered_chrs <- unique(dbReadTable(db_conn, "sample_coverage")$chr)
  depth <- dbReadTable(db_conn, "metadata")$depth
  dbDisconnect(db_conn)
  
  if (any(depth == 0)) {
      stop("Some bedgraph files were not correctly read in!\n",
           "Please call get_ssRleCov() again.")
  }

  ## only consider chromosomes with utr3 annotation and coverage
  chromosomes <- intersect(names(utr3), covered_chrs)
  chromosomes
}