def main(argv=None):

    if argv is None:
        argv = sys.argv

    try:
        optlist, args = getopt.getopt(sys.argv[1:],
                                      param_short_options,
                                      param_long_options)

    except getopt.error, msg:
        print globals()["__doc__"], msg
        sys.exit(1)

    for o, a in optlist:
        if o in ("--help",):
            print globals()["__doc__"]
            sys.exit(0)
        elif o in ("--version", ):
            print "version="
            sys.exit(0)
        elif o in ("-h", "--header-names"):
            param_headers = string.split(a, ",")
        elif o in ("-n", "--normalize"):
            param_normalize = 1
        elif o in ("-m", "--missing-value"):
            param_missing_value = a
        elif o == "--no-titles":
            param_titles = False
        elif o == "--no-titles":
            param_titles = False
        elif o in ("-f", "--format"):
            param_format = a
        elif o == "--format-value":
            param_format_value = a
        elif o == "--bin-format":
            param_format_bin = a
        elif o in ("-s", "--method=sort --sort-order"):
            if a in ("numerical", "alphabetic"):
                param_sort = a
            else:
                param_sort = string.split(a, ",")

    if len(args) < 1:
        print globals()["__doc__"], "please specify at one histogram."
        sys.exit(1)

    param_filenames = args

    print E.GetHeader()
    print E.GetParams()

    histograms = []

    # first
    headers = ['bin', ]
    if param_headers and headers != "auto":
        headers = [param_headers[0], ]
        del param_headers[0]

    for x in range(len(param_filenames)):

        filename = param_filenames[x]
        if not os.path.exists(filename):
            print "# skipped because file not present: %s" % filename
            continue

        file = open(filename, "r")

        lines = filter(lambda x: x[0] != "#", file)

        if len(lines) == 0:
            continue

        if param_titles:
            h = lines[0][:-1].split("\t")[1:]
            del lines[0]

        if param_headers == "auto":
            headers.append(os.path.basename(filename))
        elif param_headers:
            headers.append(param_headers[x])
        elif param_titles:
            headers += h

        data = map(
            lambda x: map(string.atof, string.split(x[:-1], "\t")), lines)

        # add empty data point for empty histograms
        if len(data) == 0:
            data = [(0, 0)]

        histograms.append(data)

    # sort the whole thing:
    if param_sort:
        sort_order = []

        if param_sort == "numerical":
            t = zip(map(int, headers[1:]), range(1, len(headers) + 1))
            t.sort()

            for tt in t:
                sort_order.append(headers[tt[1]])

        elif param_sort == "alphabetical":
            t = zip(headers[1:], range(1, len(headers) + 1))
            t.sort()

            for tt in t:
                sort_order.append(headers[tt[1]])
        else:
            sort_order = param_sort

        # map header to old position
        map_header2pos = {}
        for x in range(1, len(headers)):
            map_header2pos[headers[x]] = x

        order = []
        for x in sort_order:
            if x in map_header2pos:
                order.append(map_header2pos[x])

        new_headers = [headers[0]]
        new_histograms = []

        for x in order:
            new_headers.append(headers[x])
            new_histograms.append(histograms[x - 1])

        histograms = new_histograms
        headers = new_headers

    combined_histogram = Histogram.Combine(histograms, param_missing_value)

    if headers:
        print "\t".join(headers)

    if param_normalize:
        combined_histogram = Histogram.Normalize(combined_histogram)

    Histogram.Print(combined_histogram,
                    format_bin=param_format_bin,
                    format_value=param_format_value,
                    )

    print E.GetFooter()
script main.
dataset/ETHPy150Open CGATOxford/cgat/scripts/combine_histograms.py/main