R/convert_bigBed_to_bed.R

In davemcg/ChromatinCompare: Compare and analyze chromatin segmentation (ChromHMM, Segway, etc.) differences

#' Wrapper to converted bigBed to bed, using UCSC bedToBigBed tool
#'
#' @param bigBed Path to the bigBed file
#' @details You must have the UCSC bedToBigBed tool installed. UCSC provides pre-built binaries here: http://hgdownload.soe.ucsc.edu/admin/exe/. \code{convert_bigBed_to_Bed} will return the path to the converted bed file.
#'
#' @export
convert_bigBed_to_bed <- function(bigBed){
  output_bed <- paste0(strsplit(bigBed,'\\.')[[1]][1], '.bed')

  if (!file.exists(output_bed)) {
    system(paste0('bigBedToBed ', bigBed, ' ', output_bed))
    system(paste0('bgzip ', output_bed))
  }

  return(paste0(output_bed,'.gz'))
}