R/randsample.R

In macs3-project/MACSr: MACS: Model-based Analysis for ChIP-Seq

#' randsample
#'
#' Randomly sample number/percentage of total reads.
#'
#' @param ifile Alignment file. If multiple files are given as '-t A B
#'     C', then they will all be read and combined. Note that pair-end
#'     data is not supposed to work with this command. REQUIRED.
#' @param percentage Percentage of tags you want to keep. Input 80.0
#'     for 80%%. This option can't be used at the same time with
#'     -n/--num. REQUIRED
#' @param number Number of tags you want to keep. Input 8000000 or
#'     8e+6 for 8 million. This option can't be used at the same time
#'     with -p/--percent. Note that the number of tags in output is
#'     approximate as the number specified here. REQUIRED
#' @param seed Set the random seed while down sampling data. Must be a
#'     non-negative integer in order to be effective. DEFAULT: not set
#' @param tsize Tag size. This will override the auto detected tag
#'     size. DEFAULT: Not set
#' @param format Format of tag file, \"AUTO\", \"BED\" or \"ELAND\" or
#'     \"ELANDMULTI\" or \"ELANDEXPORT\" or \"SAM\" or \"BAM\" or
#'     \"BOWTIE\" or \"BAMPE\" or \"BEDPE\". The default AUTO option
#'     will %(prog)s decide which format the file is. Please check the
#'     definition in README file if you choose
#'     ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE or
#'     BAMPE/BEDPE. DEFAULT: \"AUTO\""
#' 
#' @param buffer_size Buffer size for incrementally increasing
#'     internal array size to store reads alignment information. In
#'     most cases, you don't have to change this parameter. However,
#'     if there are large number of chromosomes/contigs/scaffolds in
#'     your alignment, it's recommended to specify a smaller buffer
#'     size in order to decrease memory usage (but it will take longer
#'     time to read alignment files). Minimum memory requested for
#'     reading an alignment file is about # of CHROMOSOME *
#'     BUFFER_SIZE * 8 Bytes. DEFAULT: 100000
#' @param verbose Set verbose level. 0: only show critical message, 1:
#'     show additional warning message, 2: show process information,
#'     3: show debug messages. If you want to know where are the
#'     duplicate reads, use 3. DEFAULT:2
#' @param outputfile Output bedGraph file name. If not specified, will
#'     write to standard output. REQUIRED.
#' @param outdir The output directory.
#' @param log Whether to capture logs.
#' @return `macsList` object.
#' @export
#' @examples
#' eh <- ExperimentHub::ExperimentHub()
#' CHIP <- eh[["EH4558"]]
#' randsample(CHIP, number = 1000, outdir = tempdir(), outputfile = "randsample.bed")
randsample <- function(ifile, outdir = ".", outputfile = character(),
                       percentage = numeric(), number = numeric(),
                       seed = -1L, tsize = NULL,
                       format = c("AUTO","BAM","SAM","BED","ELAND","ELANDMULTI",
                                  "ELANDEXPORT","BOWTIE","BAMPE","BEDPE"),
                       buffer_size = 100000L, verbose = 2L, log =TRUE){
    format <- match.arg(format)
    if(is.character(ifile)){
        ifile <- as.list(normalizePath(ifile))
    }

    cl <- basiliskStart(env_macs)
    on.exit(basiliskStop(cl))
    res <- basiliskRun(cl, function(.namespace, outdir){
        opts <- .namespace()$Namespace(ifile = ifile,
                                       percentage = percentage,
                                       number = number,
                                       seed = seed,
                                       tsize = tsize,
                                       format = format,
                                       buffer_size = buffer_size,
                                       verbose = verbose,
                                       outputfile = outputfile,
                                       outdir = outdir)
        .randsample <- reticulate::import("MACS3.Commands.randsample_cmd")
        if(log){
            reticulate::py_capture_output(.randsample$run(opts))
        }else{
            .randsample$run(opts)
        }
    }, .namespace = .namespace, outdir = outdir)
    if(log){
        message(res)
    }

    ofile <- file.path(outdir, outputfile)
    args <- as.list(match.call())
    macsList(arguments = args, outputs = ofile, log = res)
}