def main(argv=None):

    if not argv:
        argv = sys.argv

    parser = E.OptionParser(
        version="%prog version: $Id: data2histogram.py 2782 2009-09-10 11:40:29Z andreas $")

    parser.add_option("-r", "--range", dest="range", type="string",
                      help="range to calculate histogram for.")
    parser.add_option("-b", "--bin-size", dest="bin_size", type="string",
                      help="bin size.")
    parser.add_option("-i", "--titles", dest="titles", action="store_true",
                      help="use supplied column titles.")
    parser.add_option("--no-null", dest="nonull", action="store_true",
                      help="do not output null values")
    parser.add_option("--no-titles", dest="titles", action="store_false",
                      help="no column titles given.")
    parser.add_option("-c", "--columns", dest="columns", type="string",
                      help="columns to take for calculating histograms.")
    parser.add_option("--min-data", dest="min_data", type="int",
                      help="minimum amount of data required, if less data, then the histogram will be empty [default=%default].")
    parser.add_option("--min-value", dest="min_value", type="float",
                      help="minimum value for histogram.")
    parser.add_option("--max-value", dest="max_value", type="float",
                      help="maximum value for histogram.")
    parser.add_option("--no-empty-bins", dest="no_empty_bins", action="store_true",
                      help="do not display empty bins.")
    parser.add_option("--with-empty-bins", dest="no_empty_bins", action="store_false",
                      help="display empty bins.")
    parser.add_option("--normalize", dest="normalize", action="store_true",
                      help="normalize histogram.")
    parser.add_option("--cumulative", dest="cumulative", action="store_true",
                      help="calculate cumulative histogram.")
    parser.add_option("--reverse-cumulative", dest="reverse_cumulative", action="store_true",
                      help="calculate reverse cumulative histogram.")
    parser.add_option("--header-names", dest="headers", type="string",
                      help="use the following headers.")
    parser.add_option("--ignore-out-of-range", dest="ignore_out_of_range", action="store_true",
                      help="ignore values that are out of range (as opposed to truncating them to range border.")
    parser.add_option("--missing-value", dest="missing_value", type="string",
                      help="entry for missing values [%default].")
    parser.add_option("--use-dynamic-bins", dest="dynamic_bins", action="store_true",
                      help="each value constitutes its own bin.")
    parser.add_option("--on-the-fly", dest="on_the_fly", action="store_true",
                      help="on the fly computation of histograms. Requires setting of min-value, max-value and bin_size.")

    parser.set_defaults(
        bin_size=None,
        range=None,
        titles=True,
        columns="all",
        append=(),
        no_empty_bins=True,
        min_value=None,
        max_value=None,
        normalize=False,
        cumulative=False,
        reverse_cumulative=False,
        nonull=None,
        ignore_out_of_range=False,
        min_data=1,
        headers=None,
        missing_value="na",
        dynamic_bins=False,
        on_the_fly=False,
        bin_format="%.2f",
        value_format="%6.4f",
    )

    (options, args) = E.Start(parser)

    if options.columns != "all":
        options.columns = map(lambda x: int(x) - 1, options.columns.split(","))

    if options.range:
        options.min_value, options.max_value = map(
            float, options.range.split(","))

    if options.headers:
        options.headers = options.headers.split(",")

    if options.on_the_fly:
        if options.min_value is None or options.max_value is None or options.bin_size is None:
            raise "please supply columns, min-value, max-value and bin-size for on-the-fly computation."

        # try to glean titles from table:
        if options.titles:
            while 1:
                line = sys.stdin.readline()
                if not line:
                    break
                if line[0] == "#":
                    continue
                data = line[:-1].split("\t")
                break

            if options.columns == "all":
                options.titles = data
                options.columns = range(len(data))
            else:
                options.titles = [data[x] for x in options.columns]

        bins = numpy.arange(
            options.min_value, options.max_value, float(options.bin_size))
        hh = Histogram.fillHistograms(
            sys.stdin, options.columns, [bins for x in range(len(options.columns))])
        n = len(hh)

        titles = ['bin']

        if options.headers:
            titles.append(options.headers[x])
        elif options.titles:
            titles.append(options.titles[x])
        else:
            for x in options.columns:
                titles.append("col%i" % (x + 1))

        if len(titles) > 1:
            options.stdout.write("\t".join(titles) + "\n")

        for x in range(len(bins)):
            v = []
            v.append(options.bin_format % bins[x])
            for c in range(n):
                v.append(options.value_format % hh[c][x])

            options.stdout.write("\t".join(v) + "\n")

    else:
        # in-situ computation of histograms
        # retrieve data
        first = True
        vals = []

        # parse data, convert to floats
        for l in options.stdin:

            if l[0] == "#":
                continue

            data = string.split(l[:-1], "\t")

            if first:
                first = False
                ncols = len(data)
                if options.columns == "all":
                    options.columns = range(ncols)

                vals = [[] for x in options.columns]

                if options.titles:
                    try:
                        options.titles = [data[x] for x in options.columns]
                    except IndexError:
                        raise IndexError, "not all columns %s found in data %s" % (
                            str(options.columns), str(data))
                    continue

            for x in range(len(options.columns)):

                try:
                    v = string.atof(data[options.columns[x]])
                except IndexError:
                    print "# IndexError in line:", l[:-1]
                    continue
                except __HOLE__:
                    continue

                vals[x].append(v)

        lines = None

        hists = []
        titles = []

        if not vals:
            if options.loglevel >= 1:
                options.stdlog.write("# no data\n")
            E.Stop()
            sys.exit(0)

        for x in range(len(options.columns)):

            if options.loglevel >= 1:
                options.stdlog.write(
                    "# column=%i, num_values=%i\n" % (options.columns[x], len(vals[x])))

            if len(vals[x]) < options.min_data:
                continue

            h = Histogram.Calculate(vals[x],
                                    no_empty_bins=options.no_empty_bins,
                                    increment=options.bin_size,
                                    min_value=options.min_value,
                                    max_value=options.max_value,
                                    dynamic_bins=options.dynamic_bins,
                                    ignore_out_of_range=options.ignore_out_of_range)

            if options.normalize:
                h = Histogram.Normalize(h)
            if options.cumulative:
                h = Histogram.Cumulate(h)
            if options.reverse_cumulative:
                h = Histogram.Cumulate(h, direction=0)

            hists.append(h)

            for m in options.append:
                if m == "normalize":
                    hists.append(Histogram.Normalize(h))

            if options.headers:
                titles.append(options.headers[x])
            elif options.titles:
                titles.append(options.titles[x])
            else:
                titles.append("col%i" % options.columns[x])

        if titles:
            options.stdout.write("bin\t" + "\t".join(titles) + "\n")

        if len(hists) == 1:
            Histogram.Print(hists[0], nonull=options.nonull)
        else:
            combined_histogram = Histogram.Combine(
                hists, missing_value=options.missing_value)
            Histogram.Print(combined_histogram, nonull=options.nonull)

    E.Stop()
dataset/ETHPy150Open CGATOxford/cgat/scripts/data2histogram.py/main