R/SamToBam.R

In esATAC: An Easy-to-use Systematic pipeline for ATACseq data analysis

setClass(Class = "SamToBam",
         contains = "ATACProc"
)


setMethod(
    f = "init",
    signature = "SamToBam",
    definition = function(.Object,prevSteps = list(), ..., samInput = NULL, bamOutput = NULL, editable = FALSE){
        atacProc <- NULL
        if(length(prevSteps)>0){
            atacProc <- prevSteps[[1]]
        }
        allparam <- list(...)
        input_file <- allparam[["input_file"]]
        output_file <- allparam[["output_file"]]
        
        # necessary parameters
        if((!is.null(atacProc)) ){
            input(.Object)[["samInput"]] <- getParam(atacProc, "samOutput")
        }else if(is.null(atacProc)){ # input
            input(.Object)[["samInput"]] <- samInput
        }
        # unnecessary parameters
        if(is.null(bamOutput)){
            param(.Object)[["name_tmp"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","" )
        
            output(.Object)[["bamOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","bam")
            output(.Object)[["baiOutput"]] <- getAutoPath(.Object, input(.Object)[["samInput"]],"sam|SAM","bam.bai")
        }else{
            bamOutput <- addFileSuffix(bamOutput,".bam")
            param(.Object)[["name_tmp"]] <- substring(bamOutput,first = 1,last = nchar(bamOutput) - 4)
            output(.Object)[["bamOutput"]] <- bamOutput
            output(.Object)[["baiOutput"]] <- addFileSuffix(bamOutput,".bai")
        }
        .Object

    }
)




setMethod(
    f = "processing",
    signature = "SamToBam",
    definition = function(.Object,...){
        Rsamtools::asBam(file = input(.Object)[["samInput"]], destination = param(.Object)[["name_tmp"]],overwrite = TRUE)
        .Object
    }
)


setMethod(
    f = "genReport",
    signature = "SamToBam",
    definition = function(.Object, ...){
        .Object
    }
)


#' @name SamToBam
#' @title Convert sam format to bam format.
#' @description
#' This function convert a sam file into a bam file.
#' @param atacProc \code{\link{ATACProc-class}} object scalar.
#' It has to be the return value of upstream process:
#' \code{\link{atacBowtie2Mapping}}.
#' @param samInput \code{Character} scalar.
#' Sam file input path.
#' @param bamOutput \code{Character} scalar.
#' Bam file output path. If ignored, bed file will be put in the same path as
#' the sam file.
#' @param ... Additional arguments, currently unused.
#' @details The sam file wiil be automatically obtained from
#' object(\code{atacProc}) or input by hand. bamOutput can be ignored.
#' @return An invisible \code{\link{ATACProc-class}} object scalar for
#' downstream analysis.
#' @author Wei Zhang
#' @examples
#'
#' library(R.utils)
#' sam_bz <- system.file("extdata", "Example.sam.bz2", package="esATAC")
#' sam_path <- as.vector(bunzip2(filename = sam_bz,
#' destname = file.path(getwd(), "Example.sam"),
#' ext="bz2", FUN=bzfile, remove = FALSE))
#' sam2bam(samInput = sam_path)
#'
#' @seealso
#' \code{\link{atacBowtie2Mapping}}
#' \code{\link{atacBam2Bed}}
#' \code{\link{atacBamSort}}


setGeneric("atacSam2Bam",function(atacProc,
                                  samInput = NULL, bamOutput = NULL, ...) standardGeneric("atacSam2Bam"))
#' @rdname SamToBam
#' @aliases atacSam2Bam
#' @export
setMethod(
    f = "atacSam2Bam",
    signature = "ATACProc",
    definition = function(atacProc,
                          samInput = NULL, bamOutput = NULL, ...){
        allpara <- c(list(Class = "SamToBam", prevSteps = list(atacProc)),as.list(environment()),list(...))
        step <- do.call(new,allpara)
        invisible(step)
    }
)
#' @rdname SamToBam
#' @aliases sam2bam
#' @export
sam2bam <- function(samInput, bamOutput = NULL, ...){
    allpara <- c(list(Class = "SamToBam", prevSteps = list()),as.list(environment()),list(...))
    step <- do.call(new,allpara)
    invisible(step)
}