R/base_constructExtRead.R

In dpeak: dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

# read alignment files and construct bin-level files

.constructExtRead <- function( infile=NULL, outfile=NULL, summaryfile=NULL,
    fileFormat="eland_result", PET=FALSE, fragLen=200, perl = "perl" )
{
    # preprocessing perl script embedded in "dpeak/inst/Perl/"

    if ( PET ) {
        script <- "extract_coord_PET.pl"
        allFormat <- "eland_result"
        allFormatName <- "Eland result"
    } else {
        script <- "extract_coord_SET.pl"
        allFormat <- c( "eland_result", "eland_extended", "eland_export", "bowtie", "sam", "bed" )
        allFormatName <- c( "Eland result", "Eland extended", "Eland export", "Bowtie default", "SAM", "BED" )
    }

    # Check whether perl exists

    CMD <- paste( perl, "-v" )
    res <- system( CMD, intern = TRUE, ignore.stderr = TRUE )

    if ( length(res) == 0 ) {
        # cannot proceed if perl does not exist

        stop( "Perl is not found on your system. Either check $PATH if installed or please install Perl." )
    } else {
        # process read files into bin-level files if perl exists

        # check whether minimal options are missing

        if ( length(infile) != 1 || is.null(infile) )
        {
            stop( "Please specify the aligned read file." )
        }

        if ( length(fileFormat) != 1 || is.null(fileFormat) )
        {
            stop( "Please specify aligned read file format. Read '?constructExtRead' for supported file formats" )
        }

        # check file format specification

        if ( length(which(!is.na(match( fileFormat, allFormat )))) == 0 )
        {
            stop( "Unsupported aligned read file format Read '?constructExtRead' for supported file formats" )
        }

        fileFormatName <- allFormatName[ match( fileFormat, allFormat ) ]


        # get path to the perl code (unified script for all file formats)

        Fn.Path <- system.file( file.path("Perl",script), package="dpeak" )


        # process read file to bin-level files using perl codes

        if ( PET ) {
            CMD <- paste( perl,
                " ", Fn.Path,
                " ", infile,
                " ", outfile,
                " ", summaryfile,
                " ", fileFormat, sep="" )
        } else {
            CMD <- paste( perl,
                " ", Fn.Path,
                " ", infile,
                " ", outfile,
                " ", summaryfile,
                " ", fileFormat,
                " ", fragLen, sep="" )
        }

        res <- system( CMD, intern = TRUE )
    }
}