<gh_stars>0
#!/usr/bin/env python

from optparse import OptionParser, OptionGroup, SUPPRESS_HELP
import os
import sys

from mapdamage.version import __version__
from mapdamage.rscript import check_R_lib

def file_exist(filename):
    if os.path.exists(filename) and not os.path.isdir(filename):
        return True
    elif filename == "-":
        return True
    else:
        sys.stderr.write("Error: '%s' is not a valid file\n" % (filename))
        return None


def whereis(program):
    for path in os.environ.get('PATH', '').split(':'):
        if os.path.exists(os.path.join(path, program)) and \
            not os.path.isdir(os.path.join(path, program)):
            return os.path.join(path, program)
    return None



def check_py_version():
    req_version = (2, 6)
    cur_version = sys.version_info

    if cur_version >= req_version:
        return True
    else:
        sys.stderr.write("Your Python interpreter is too old."\
            "Please consider upgrading to at least %d.%d\n" % (req_version[0], req_version[1]))
        return None


def options():  
    parser = OptionParser("%prog [options] -i BAMfile -r reference.fasta\n\nUse option -h or --help for help", version=__version__, \
            epilog="report bugs to <EMAIL>, <EMAIL> or <EMAIL>")

    args = OptionGroup(parser, "Input files")
    args.add_option("-i", "--input", help="SAM/BAM file, must contain a valid header, use '-' for reading a BAM from stdin", \
          action="store", type="string", dest="filename")
    args.add_option("-r", "--reference", help="Reference file in FASTA format", \
          action="store", dest="ref")

    parser.add_option_group(args)
    group = OptionGroup(parser, "General options")
    group.add_option("-n", "--downsample", help = "Downsample to a randomly selected fraction of the reads (if 0 < DOWNSAMPLE < 1), or " \
                     "a fixed number of randomly selected reads (if DOWNSAMPLE >= 1). By default, no downsampling is performed.",
                     type = float, default = None)
    group.add_option("--downsample-seed", help = "Seed value to use for downsampling. See documentation for py module 'random' for default behavior.",
                     type = int, default = None)
    group.add_option("--merge-reference-sequences", help = "Ignore referece sequence names when tabulating reads (using '*' instead). "
                     "Useful for alignments with a large number of reference sequnces, which may otherwise result in excessive "
                     "memory or disk usage due to the number of tables generated.",
                     default = False, action = "store_true")
    group.add_option("-l", "--length", dest="length", help="read length, in nucleotides to consider [%default]", \
            type = int, default=70,action="store")
    group.add_option("-a", "--around", dest="around", help="nucleotides to retrieve before/after reads [%default]", \
            type = int, default=10,action="store")
    group.add_option("-Q", "--min-basequal", dest="minqual", help="minimun base quality Phred score considered, Phred-33 assumed [%default]", \
            type = int, default=0, action="store")
    group.add_option("-d", "--folder", help="folder name to store results [results_FILENAME]", \
          action="store", type="string", dest="folder")
    group.add_option("-f", "--fasta", dest="fasta", help="Write alignments in a FASTA file", \
          default=False,action="store_true")
    group.add_option("--plot-only", dest="plot_only", help="Run only plotting from a valid result folder", \
          default=False,action="store_true")
    group.add_option("-q", "--quiet", dest="quiet", help="Disable any output to stdout", \
          default=False,action="store_true")
    group.add_option("-v", "--verbose", dest="verbose", help="Display progression information during parsing", \
          default=False,action="store_true")
    group.add_option("--mapdamage-modules", dest="mapdamage_modules", help="Override the system wide installed mapDamage module", \
          default=None)
    group.add_option("--no-plot", dest="no_r", help=SUPPRESS_HELP, default=False, action="store_true")
    parser.add_option_group(group)

    # options for plotting damage patterns
    group2 = OptionGroup(parser, "Options for graphics")
    group2.add_option("-y", "--ymax", dest="ymax", \
           help="graphical y-axis limit for nucleotide misincorporation frequencies [%default]", type = float, \
           default=0.3,action="store")
    group2.add_option("-m", "--readplot", dest="readplot", \
           help="read length, in nucleotides, considered for plotting nucleotide misincorporations [%default]", \
           type = int, default=25, action="store")
    group2.add_option("-b", "--refplot", dest="refplot", \
          help="the number of reference nucleotides to consider for ploting base composition in the region located upstream "
          "and downstream of every read [%default]", type= int, default=10, action="store")
    group2.add_option("-t", "--title", dest="title", \
          help="title used for plots [%default]", \
          type="string", default="",action="store")
    parser.add_option_group(group2)

    # Then the plethora of optional options for the statistical estimation ..
    group3 = OptionGroup(parser,"Options for the statistical estimation")
    group3.add_option("", "--rand", dest="rand", \
            help="Number of random starting points for the likelihood optimization  [%default]", type = int, default=30, action="store")
    group3.add_option("", "--burn", dest="burn", \
            help="Number of burnin iterations  [%default]", type = int, default=10000,action="store")
    group3.add_option("", "--adjust", dest="adjust", \
            help="Number of adjust proposal variance parameters iterations  [%default]", type = int, default=10, action="store")
    group3.add_option("", "--iter", dest="iter", \
            help="Number of final MCMC iterations  [%default]", type = int, default=50000, action="store")
    group3.add_option("", "--forward", dest="forward", \
            help="Using only the 5' end of the seqs  [%default]", default=False, action="store_true")
    group3.add_option("", "--reverse", dest="reverse", \
            help="Using only the 3' end of the seqs  [%default]", default=False, action="store_true")
    group3.add_option("", "--var-disp", dest="var_disp", \
            help="Variable dispersion in the overhangs  [%default]", default=False,action="store_true")
    group3.add_option("", "--jukes-cantor", dest="jukes_cantor", \
            help="Use Jukes Cantor instead of HKY85  [%default]", default=False,action="store_true")
    group3.add_option("", "--diff-hangs", dest="diff_hangs", \
            help="The overhangs are different for 5' and 3'  [%default]", default=False, action="store_true")
    group3.add_option("", "--fix-nicks" , dest="fix_nicks", \
            help="Fix the nick frequency vector (Only C.T from the 5' end and G.A from the 3' end)  [%default]", default=False, action="store_true")
    group3.add_option("", "--use-raw-nick-freq" , dest="use_raw_nick_freq", \
            help="Use the raw nick frequency vector without smoothing  [%default]", default=False, action="store_true")
    group3.add_option("", "--single-stranded", dest="single_stranded", \
            help="Single stranded protocol [%default]", default=False, action="store_true")
    group3.add_option("", "--theme-bw", dest="theme_bw", \
            help="Use black and white theme in post. pred. plot [%default]", default=False, action="store_true")
    group3.add_option("", "--seq-length", dest="seq_length", \
            help="How long sequence to use from each side [%default]", type = int, default=12, action="store")
    group3.add_option("--stats-only", dest="stats_only", help="Run only statistical estimation from a valid result folder", \
          default=False, action="store_true")
    group3.add_option("--no-stats", help="Disabled statistical estimation, active by default", default=False, action="store_true")
    group3.add_option("--check-R-packages", help="Check if the R modules are working", default=False, action="store_true")
    parser.add_option_group(group3)

    group4 = OptionGroup(parser,"Options for rescaling of BAM files")
    group4.add_option("--rescale", dest="rescale", help="Rescale the quality scores in the BAM file using the output from the statistical estimation",
          default=False, action="store_true")
    group4.add_option("--rescale-only", dest="rescale_only", help="Run only rescaling from a valid result folder",
          default=False, action="store_true")
    group4.add_option("--rescale-out", dest="rescale_out", help="Write the rescaled BAM to this file",
          default=None, action="store")
    group4.add_option("--rescale-length-5p", dest="rescale_length_5p",
                      help="How many bases to rescale at the 5' termini; defaults to --seq-length.", type=int, action="store")
    group4.add_option("--rescale-length-3p", dest="rescale_length_3p",
                      help="How many bases to rescale at the 5' termini; defaults to --seq-length.", type=int, action="store")
    parser.add_option_group(group4)


    #Parse the arguments
    (options, args) = parser.parse_args()

    # check python version
    if not check_py_version():
        return None

    # if the user wants to check the R packages then do that before the option parsing 
    if options.check_R_packages:
        if check_R_lib():
            sys.exit(1)
        else:
            print("All R packages are present")
            sys.exit(0)

    # check general arguments
    if not (options.plot_only or options.stats_only) and not options.filename:
        parser.error('SAM/BAM file not given (-i)')
    if not (options.plot_only or options.ref):
        parser.error('Reference file not given (-r)')
    if not options.plot_only and not options.stats_only:
        if not file_exist(options.filename) or not file_exist(options.ref):
            return None
    if options.downsample is not None:
        if options.downsample <= 0:
            parser.error("-n/--downsample must be a positive value")
        elif options.downsample >= 1:
            options.downsample = int(options.downsample)

    if options.plot_only and not options.folder:
        parser.error('Folder not provided, required with --plot-only')
    if options.stats_only and not options.folder:
        parser.error('Folder not provided, required with --stats-only')
    if options.rescale_only and not options.folder:
        parser.error('Folder not provided, required with --rescale-only')
    if options.rescale_only and not options.filename:
        parser.error('Input bam not provided, required with --rescale-only')
    if options.rescale_only and not options.ref:
        parser.error('Reference not provided, required with --rescale-only')

    if options.verbose and options.quiet:
        parser.error('Cannot use verbose and quiet option at the same time')

    # check options
    if options.length < 0:
        parser.error('length (-l) must be a positive integrer')
    if options.around < 0:
        parser.error('around (-a) must be a positive integrer')
    if options.ymax <= 0 or options.ymax > 1:
        parser.error('ymax (-b) must be an real number beetween 0 and 1')
    if options.readplot < 0:
        parser.error('readplot (-m) must be a positive integrer')
    if options.refplot < 0:
        parser.error('refplot (-b) must be a positive integrer')
    if options.refplot > options.around and not options.plot_only:
        parser.error('refplot (-b) must be inferior to around (-a)')
    if options.readplot > options.length:
        parser.error('readplot (-m) must be inferior to length (-l)')
    if options.minqual < 0 or  options.minqual > 41:
        parser.error('minimal base quality, Phred score, must be within this range: 0 - 41')

    # check statistic options
    if options.forward and options.reverse:
        parser.error('Cannot use only forward end and only reverse end for the statistics')

    # use filename as default for plot titles if not set
    if options.title == "" and options.filename:
        options.title = os.path.splitext(os.path.basename(options.filename))[0]
    # for --plot-only, use the folder name, without results_ as title
    if options.title == "" and not options.filename and options.folder:
        options.title = os.path.splitext(os.path.basename(options.folder))[0].replace("results_", "")

    # check folder
    if not options.folder and options.filename:
        options.folder = "results_"+os.path.splitext(os.path.basename(options.filename))[0]

    # check destination for rescaled bam
    if not options.rescale_out and (options.rescale or options.rescale_only):
        # if there are mulitiple bam files to rescale then pick first one as 
        # the name of the rescaled file
        if isinstance(options.filename,list):
            basename = os.path.basename(options.filename[0])
        else:
            basename = os.path.basename(options.filename)
        with_ext = os.path.splitext(basename)[0] + ".rescaled.bam"
        options.rescale_out = os.path.join(options.folder, with_ext)

    if os.path.isdir(options.folder):
        if not options.quiet and not options.plot_only:
            print("Warning, %s already exists" % options.folder)
        if options.plot_only:
            if not file_exist(options.folder+"/dnacomp.txt") or not file_exist(options.folder+"/misincorporation.txt"):
                parser.error('folder %s is not a valid result folder' % options.folder)
    else:
        os.makedirs(options.folder, mode = 0750)
        if options.plot_only or options.stats_only or options.rescale_only:
            sys.stderr.write("Error, %s does not exist while plot/stats/rescale only was used\n" % options.folder)
            return None

    if options.rescale_length_3p is None:
        options.rescale_length_3p = options.seq_length
    elif not (0 <= options.rescale_length_3p <= options.seq_length):
        parser.error("--rescale-length-3p must be less than or equal to "
                     "--seq-length and greater than zero")

    if options.rescale_length_5p is None:
        options.rescale_length_5p = options.seq_length
    elif not (0 <= options.rescale_length_5p <= options.seq_length):
        parser.error("--rescale-length-5p must be less than or equal to "
                     "--seq-length and greater than zero")

    # check if the Rscript executable is present on the system
    if not whereis('Rscript'):
        print("Warning, Rscript is not in your PATH, plotting is disabled")
        options.no_r = True

    # check the nick frequencies options
    if (options.use_raw_nick_freq + options.fix_nicks + options.single_stranded)>1:
        parser.error("The options --use-raw-nick-freq, --fix-nicks and --single-stranded are mutually exclusive.")

    if check_R_lib():
        # check for R libraries
        print("The Bayesian estimation has been disabled\n")
        options.no_stats = True
        if options.stats_only:
            sys.exit("Cannot use --stats-only with missing R libraries")
        if options.rescale:
            sys.exit("Cannot use --rescale with missing R libraries")
        if options.rescale_only:
            sys.exit("Cannot use --rescale-only with missing R libraries")


    return options


#!/usr/bin/env python

from optparse import OptionParser, OptionGroup, SUPPRESS_HELP
import os
import sys

from mapdamage.version import __version__
from mapdamage.rscript import check_R_lib

def file_exist(filename):
    if os.path.exists(filename) and not os.path.isdir(filename):
        return True
    elif filename == "-":
        return True
    else:
        sys.stderr.write("Error: '%s' is not a valid file\n" % (filename))
        return None


def whereis(program):
    for path in os.environ.get('PATH', '').split(':'):
        if os.path.exists(os.path.join(path, program)) and \
            not os.path.isdir(os.path.join(path, program)):
            return os.path.join(path, program)
    return None



def check_py_version():
    req_version = (2, 6)
    cur_version = sys.version_info

    if cur_version >= req_version:
        return True
    else:
        sys.stderr.write("Your Python interpreter is too old."\
            "Please consider upgrading to at least %d.%d\n" % (req_version[0], req_version[1]))
        return None


def options():  
    parser = OptionParser("%prog [options] -i BAMfile -r reference.fasta\n\nUse option -h or --help for help", version=__version__, \
            epilog="report bugs to <EMAIL>, <EMAIL> or <EMAIL>")

    args = OptionGroup(parser, "Input files")
    args.add_option("-i", "--input", help="SAM/BAM file, must contain a valid header, use '-' for reading a BAM from stdin", \
          action="store", type="string", dest="filename")
    args.add_option("-r", "--reference", help="Reference file in FASTA format", \
          action="store", dest="ref")

    parser.add_option_group(args)
    group = OptionGroup(parser, "General options")
    group.add_option("-n", "--downsample", help = "Downsample to a randomly selected fraction of the reads (if 0 < DOWNSAMPLE < 1), or " \
                     "a fixed number of randomly selected reads (if DOWNSAMPLE >= 1). By default, no downsampling is performed.",
                     type = float, default = None)
    group.add_option("--downsample-seed", help = "Seed value to use for downsampling. See documentation for py module 'random' for default behavior.",
                     type = int, default = None)
    group.add_option("--merge-reference-sequences", help = "Ignore referece sequence names when tabulating reads (using '*' instead). "
                     "Useful for alignments with a large number of reference sequnces, which may otherwise result in excessive "
                     "memory or disk usage due to the number of tables generated.",
                     default = False, action = "store_true")
    group.add_option("-l", "--length", dest="length", help="read length, in nucleotides to consider [%default]", \
            type = int, default=70,action="store")
    group.add_option("-a", "--around", dest="around", help="nucleotides to retrieve before/after reads [%default]", \
            type = int, default=10,action="store")
    group.add_option("-Q", "--min-basequal", dest="minqual", help="minimun base quality Phred score considered, Phred-33 assumed [%default]", \
            type = int, default=0, action="store")
    group.add_option("-d", "--folder", help="folder name to store results [results_FILENAME]", \
          action="store", type="string", dest="folder")
    group.add_option("-f", "--fasta", dest="fasta", help="Write alignments in a FASTA file", \
          default=False,action="store_true")
    group.add_option("--plot-only", dest="plot_only", help="Run only plotting from a valid result folder", \
          default=False,action="store_true")
    group.add_option("-q", "--quiet", dest="quiet", help="Disable any output to stdout", \
          default=False,action="store_true")
    group.add_option("-v", "--verbose", dest="verbose", help="Display progression information during parsing", \
          default=False,action="store_true")
    group.add_option("--mapdamage-modules", dest="mapdamage_modules", help="Override the system wide installed mapDamage module", \
          default=None)
    group.add_option("--no-plot", dest="no_r", help=SUPPRESS_HELP, default=False, action="store_true")
    parser.add_option_group(group)

    # options for plotting damage patterns
    group2 = OptionGroup(parser, "Options for graphics")
    group2.add_option("-y", "--ymax", dest="ymax", \
           help="graphical y-axis limit for nucleotide misincorporation frequencies [%default]", type = float, \
           default=0.3,action="store")
    group2.add_option("-m", "--readplot", dest="readplot", \
           help="read length, in nucleotides, considered for plotting nucleotide misincorporations [%default]", \
           type = int, default=25, action="store")
    group2.add_option("-b", "--refplot", dest="refplot", \
          help="the number of reference nucleotides to consider for ploting base composition in the region located upstream "
          "and downstream of every read [%default]", type= int, default=10, action="store")
    group2.add_option("-t", "--title", dest="title", \
          help="title used for plots [%default]", \
          type="string", default="",action="store")
    parser.add_option_group(group2)

    # Then the plethora of optional options for the statistical estimation ..
    group3 = OptionGroup(parser,"Options for the statistical estimation")
    group3.add_option("", "--rand", dest="rand", \
            help="Number of random starting points for the likelihood optimization  [%default]", type = int, default=30, action="store")
    group3.add_option("", "--burn", dest="burn", \
            help="Number of burnin iterations  [%default]", type = int, default=10000,action="store")
    group3.add_option("", "--adjust", dest="adjust", \
            help="Number of adjust proposal variance parameters iterations  [%default]", type = int, default=10, action="store")
    group3.add_option("", "--iter", dest="iter", \
            help="Number of final MCMC iterations  [%default]", type = int, default=50000, action="store")
    group3.add_option("", "--forward", dest="forward", \
            help="Using only the 5' end of the seqs  [%default]", default=False, action="store_true")
    group3.add_option("", "--reverse", dest="reverse", \
            help="Using only the 3' end of the seqs  [%default]", default=False, action="store_true")
    group3.add_option("", "--var-disp", dest="var_disp", \
            help="Variable dispersion in the overhangs  [%default]", default=False,action="store_true")
    group3.add_option("", "--jukes-cantor", dest="jukes_cantor", \
            help="Use Jukes Cantor instead of HKY85  [%default]", default=False,action="store_true")
    group3.add_option("", "--diff-hangs", dest="diff_hangs", \
            help="The overhangs are different for 5' and 3'  [%default]", default=False, action="store_true")
    group3.add_option("", "--fix-nicks" , dest="fix_nicks", \
            help="Fix the nick frequency vector (Only C.T from the 5' end and G.A from the 3' end)  [%default]", default=False, action="store_true")
    group3.add_option("", "--use-raw-nick-freq" , dest="use_raw_nick_freq", \
            help="Use the raw nick frequency vector without smoothing  [%default]", default=False, action="store_true")
    group3.add_option("", "--single-stranded", dest="single_stranded", \
            help="Single stranded protocol [%default]", default=False, action="store_true")
    group3.add_option("", "--theme-bw", dest="theme_bw", \
            help="Use black and white theme in post. pred. plot [%default]", default=False, action="store_true")
    group3.add_option("", "--seq-length", dest="seq_length", \
            help="How long sequence to use from each side [%default]", type = int, default=12, action="store")
    group3.add_option("--stats-only", dest="stats_only", help="Run only statistical estimation from a valid result folder", \
          default=False, action="store_true")
    group3.add_option("--no-stats", help="Disabled statistical estimation, active by default", default=False, action="store_true")
    group3.add_option("--check-R-packages", help="Check if the R modules are working", default=False, action="store_true")
    parser.add_option_group(group3)

    group4 = OptionGroup(parser,"Options for rescaling of BAM files")
    group4.add_option("--rescale", dest="rescale", help="Rescale the quality scores in the BAM file using the output from the statistical estimation",
          default=False, action="store_true")
    group4.add_option("--rescale-only", dest="rescale_only", help="Run only rescaling from a valid result folder",
          default=False, action="store_true")
    group4.add_option("--rescale-out", dest="rescale_out", help="Write the rescaled BAM to this file",
          default=None, action="store")
    group4.add_option("--rescale-length-5p", dest="rescale_length_5p",
                      help="How many bases to rescale at the 5' termini; defaults to --seq-length.", type=int, action="store")
    group4.add_option("--rescale-length-3p", dest="rescale_length_3p",
                      help="How many bases to rescale at the 5' termini; defaults to --seq-length.", type=int, action="store")
    parser.add_option_group(group4)


    #Parse the arguments
    (options, args) = parser.parse_args()

    # check python version
    if not check_py_version():
        return None

    # if the user wants to check the R packages then do that before the option parsing 
    if options.check_R_packages:
        if check_R_lib():
            sys.exit(1)
        else:
            print("All R packages are present")
            sys.exit(0)

    # check general arguments
    if not (options.plot_only or options.stats_only) and not options.filename:
        parser.error('SAM/BAM file not given (-i)')
    if not (options.plot_only or options.ref):
        parser.error('Reference file not given (-r)')
    if not options.plot_only and not options.stats_only:
        if not file_exist(options.filename) or not file_exist(options.ref):
            return None
    if options.downsample is not None:
        if options.downsample <= 0:
            parser.error("-n/--downsample must be a positive value")
        elif options.downsample >= 1:
            options.downsample = int(options.downsample)

    if options.plot_only and not options.folder:
        parser.error('Folder not provided, required with --plot-only')
    if options.stats_only and not options.folder:
        parser.error('Folder not provided, required with --stats-only')
    if options.rescale_only and not options.folder:
        parser.error('Folder not provided, required with --rescale-only')
    if options.rescale_only and not options.filename:
        parser.error('Input bam not provided, required with --rescale-only')
    if options.rescale_only and not options.ref:
        parser.error('Reference not provided, required with --rescale-only')

    if options.verbose and options.quiet:
        parser.error('Cannot use verbose and quiet option at the same time')

    # check options
    if options.length < 0:
        parser.error('length (-l) must be a positive integrer')
    if options.around < 0:
        parser.error('around (-a) must be a positive integrer')
    if options.ymax <= 0 or options.ymax > 1:
        parser.error('ymax (-b) must be an real number beetween 0 and 1')
    if options.readplot < 0:
        parser.error('readplot (-m) must be a positive integrer')
    if options.refplot < 0:
        parser.error('refplot (-b) must be a positive integrer')
    if options.refplot > options.around and not options.plot_only:
        parser.error('refplot (-b) must be inferior to around (-a)')
    if options.readplot > options.length:
        parser.error('readplot (-m) must be inferior to length (-l)')
    if options.minqual < 0 or  options.minqual > 41:
        parser.error('minimal base quality, Phred score, must be within this range: 0 - 41')

    # check statistic options
    if options.forward and options.reverse:
        parser.error('Cannot use only forward end and only reverse end for the statistics')

    # use filename as default for plot titles if not set
    if options.title == "" and options.filename:
        options.title = os.path.splitext(os.path.basename(options.filename))[0]
    # for --plot-only, use the folder name, without results_ as title
    if options.title == "" and not options.filename and options.folder:
        options.title = os.path.splitext(os.path.basename(options.folder))[0].replace("results_", "")

    # check folder
    if not options.folder and options.filename:
        options.folder = "results_"+os.path.splitext(os.path.basename(options.filename))[0]

    # check destination for rescaled bam
    if not options.rescale_out and (options.rescale or options.rescale_only):
        # if there are mulitiple bam files to rescale then pick first one as 
        # the name of the rescaled file
        if isinstance(options.filename,list):
            basename = os.path.basename(options.filename[0])
        else:
            basename = os.path.basename(options.filename)
        with_ext = os.path.splitext(basename)[0] + ".rescaled.bam"
        options.rescale_out = os.path.join(options.folder, with_ext)

    if os.path.isdir(options.folder):
        if not options.quiet and not options.plot_only:
            print("Warning, %s already exists" % options.folder)
        if options.plot_only:
            if not file_exist(options.folder+"/dnacomp.txt") or not file_exist(options.folder+"/misincorporation.txt"):
                parser.error('folder %s is not a valid result folder' % options.folder)
    else:
        os.makedirs(options.folder, mode = 0750)
        if options.plot_only or options.stats_only or options.rescale_only:
            sys.stderr.write("Error, %s does not exist while plot/stats/rescale only was used\n" % options.folder)
            return None

    if options.rescale_length_3p is None:
        options.rescale_length_3p = options.seq_length
    elif not (0 <= options.rescale_length_3p <= options.seq_length):
        parser.error("--rescale-length-3p must be less than or equal to "
                     "--seq-length and greater than zero")

    if options.rescale_length_5p is None:
        options.rescale_length_5p = options.seq_length
    elif not (0 <= options.rescale_length_5p <= options.seq_length):
        parser.error("--rescale-length-5p must be less than or equal to "
                     "--seq-length and greater than zero")

    # check if the Rscript executable is present on the system
    if not whereis('Rscript'):
        print("Warning, Rscript is not in your PATH, plotting is disabled")
        options.no_r = True

    # check the nick frequencies options
    if (options.use_raw_nick_freq + options.fix_nicks + options.single_stranded)>1:
        parser.error("The options --use-raw-nick-freq, --fix-nicks and --single-stranded are mutually exclusive.")

    if check_R_lib():
        # check for R libraries
        print("The Bayesian estimation has been disabled\n")
        options.no_stats = True
        if options.stats_only:
            sys.exit("Cannot use --stats-only with missing R libraries")
        if options.rescale:
            sys.exit("Cannot use --rescale with missing R libraries")
        if options.rescale_only:
            sys.exit("Cannot use --rescale-only with missing R libraries")


    return options
#!/usr/bin/env python # options for plotting damage patterns # Then the plethora of optional options for the statistical estimation .. #Parse the arguments # check python version # if the user wants to check the R packages then do that before the option parsing # check general arguments # check options # check statistic options # use filename as default for plot titles if not set # for --plot-only, use the folder name, without results_ as title # check folder # check destination for rescaled bam # if there are mulitiple bam files to rescale then pick first one as # the name of the rescaled file # check if the Rscript executable is present on the system # check the nick frequencies options # check for R libraries