R/AromaUgpFile.XTRAS.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

setMethodS3("anyDuplicated", "AromaUgpFile", function(x, ...) {
  # To please R CMD check
  this <- x
  data <- readDataFrame(this, ...)
  anyDuplicated(data, ...)
})


setMethodS3("writeBedDataFile", "AromaUgpFile", function(this, ..., path=getPath(this), chrMap=NULL, skip=TRUE, overwrite=!skip, verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
  # Argument 'chrMap':
  if (!is.null(chrMap)) {
    chrMap <- Arguments$getIndices(chrMap, useNames=TRUE)
    if (is.null(names(chrMap))) {
      throw("Argument 'chrMap' should have names.")
    }
  }

  # Argument 'skip':
  skip <- Arguments$getLogical(skip)

  # Argument 'overwrite':
  overwrite <- Arguments$getLogical(overwrite)

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }


  verbose && enter(verbose, "Exporting UGP as BED file")
  filename <- sprintf("%s.bed", getFilename(this))
  pathname <- Arguments$getReadablePathname(filename, path=path, mustExist=FALSE)
  verbose && cat(verbose, "UGP pathname: ", getPathname(this))
  verbose && cat(verbose, "BED pathname: ", pathname)

  # Already done?
  if (skip && isFile(pathname)) {
    verbose && cat(verbose, "Already exported. Skipping.")
    res <- GenericDataFile(pathname)
    verbose && print(verbose, res)
    verbose && exit(verbose)
    return(invisible(res))
  }

  pathname <- Arguments$getWritablePathname(pathname, mustNotExist=!overwrite)

  verbose && enter(verbose, "Reading data")
  data <- readDataFrame(this, verbose=less(verbose, 10))
  verbose && str(verbose, data)
  verbose && exit(verbose)

  if (!is.null(chrMap)) {
    verbose && enter(verbose, "Renaming chromosomes")
    verbose && print(verbose, chrMap)
    keys <- names(chrMap)
    chrs <- data$chromosome
    for (kk in seq_along(keys)) {
      key <- keys[kk]
      chr <- chrMap[kk]
      idxs <- which(chrs == chr)
      if (length(idxs) > 0L) {
        chrs[idxs] <- key
      }
    }
    data$chromosome <- chrs
    # Not needed anymore
    rm(keys, chrs)
    verbose && exit(verbose)
  }

  verbose && enter(verbose, "Writing BED file")
  pathnameD <- writeDataFrame(data, file=pathname, col.names=FALSE, header=NULL)
  verbose && exit(verbose)

  # Not needed anymore
  rm(data)

  res <- GenericDataFile(pathname)
  verbose && print(verbose, res)

  verbose && exit(verbose)

  invisible(res)
}) # writeBedDataFile()