R/CleanBAMtoBG.R

In nearBynding: Discern RNA structure proximal to protein binding

#' @title CleanBAMtoBG
#'
#' @description Writes a script to convert a BAM file to a clean bedGraph file.
#'
#' @param in_bam Name of sorted BAM file to be converted to a bedGraph file.
#' Required.
#' @param out_bedGraph Name of bedGraph output file, including full directory
#' path. Default in_bam prefix.
#' @param unwanted_chromosomes A vector of unwanted chromosomes that are present
#' in the BAM file.
#'
#' @return deposits bedGraph from BAM in same directory
#'
#' @examples
#' bam <- system.file("extdata/chr4and5.bam", package="nearBynding")
#' #sort BAM first
#' sorted_bam<-Rsamtools::sortBam(bam, "chr4and5_sorted")
#' CleanBAMtoBG(in_bam = sorted_bam)
#'
#' \donttest{
#'     ## If BAM has unwanted chromosome "EBV"
#'     ## this file is from ENCODE database
#'     CleanBAMtoBG(in_bam = "ENCFF288LEG.bam",
#'                  unwanted_chromosomes = "EBV")
#' }
#'
#' @importFrom Rsamtools indexBam idxstatsBam filterBam ScanBamParam
#' @importFrom magrittr '%>%'
#' @importFrom S4Vectors FilterRules
#'
#'
#' @export

CleanBAMtoBG <- function(in_bam, out_bedGraph = NA,
                        unwanted_chromosomes = NULL) {
    if (is.na(out_bedGraph)) {
        out_bedGraph <- paste0(substr(in_bam, 0, nchar(in_bam) - 3), "bedGraph")
    }
    indexBam(in_bam)
    if (length(unwanted_chromosomes) > 0) {
        tmp <- tempfile(tmpdir = ".")
        hold <- idxstatsBam(in_bam) %>% dplyr::select(1) %>%
            unlist() %>% as.vector()
        matches <- unique(grep(paste(unwanted_chromosomes,collapse = "|"),
                                    hold, value = TRUE, invert = TRUE))
        filter <- FilterRules(list(reads = function(x) x$rname %in%
                                    matches))
        filterBam(in_bam, tmp, param = ScanBamParam(what = "rname"),
                                    filter = filter)
        if(.is_bedtools_installed()){
            .bedtools_run(paste0("genomecov -ibam ",
                                    tmp, " -bg > ", out_bedGraph))
        } else{return("Please install bedtools and place in working PATH")}
        unlink(tmp)
        unlink(paste0(tmp, ".bai"))
    } else {
        if(.is_bedtools_installed()){
            .bedtools_run(paste0("genomecov -ibam ",
                                    in_bam, " -bg > ", out_bedGraph))
        } else{return("Please install bedtools and place in working PATH")}
    }
}