How to use the pygtftk.utils.VERBOSITY function in pygtftk

# to the system
        if pygtftk.__NON_INTERACTIVE__:
            message("Error encountered. System will exit after deleting temporary files.", type="DEBUG")

            if not pygtftk.__ARGS__['keep_all']:
                for i in flatten_list(TMP_FILE_LIST, outlist=[]):
                    message("ERROR encountered, deleting temporary file: " + i, type="DEBUG")
                    silentremove(i)
            else:
                message("Deletion of temporary files canceled by user.", type="DEBUG")
            sys.exit(1)
        else:
            raise GTFtkInteractiveError(msg)

    if force:
        pygtftk.utils.VERBOSITY = VERBOSITY_BACK

def message(msg, nl=True, type="INFO", force=False):
    """Send a formated message on STDERR.

    :param msg: the message to be send.
    :param nl: if True, add a newline.
    :param type: Could be INFO, ERROR, WARNING.
    :param force: Force message, whatever the verbosity level.


    >>> from pygtftk.utils import message
    """

    now = datetime.datetime.now()

    if pygtftk.utils.VERBOSITY > 2:
        ho_min = str(now.hour) + ":" + str(now.minute).zfill(2) + ":" + str(now.second).zfill(2)
    else:
        ho_min = str(now.hour) + ":" + str(now.minute).zfill(2)

    do_it = False

    if type not in ["INFO", "ERROR", "WARNING", "DEBUG", "DEBUG_MEM"]:
        raise GTFtkError(
            "Type should be one of INFO, ERROR, WARNING, DEBUG, DEBUG_MEM.")

    if force:
        VERBOSITY_BACK = pygtftk.utils.VERBOSITY
        pygtftk.utils.VERBOSITY = 2

    if pygtftk.utils.VERBOSITY >= 2:
        do_it = True

'txt': txt_regexp,
                      'txt.gz': txt_regexp_gz,
                      'bigwig': bigwig_regexp,
                      'zip': zip_regexp,
                      'pdf': pdf_regexp}

        # Set verbosity system wide as depending on
        # command line argument order, VERBOSITY (-V) can
        # be evaluated later...
        if '-V' in sys.argv:
            sys_args = ' '.join(sys.argv)
            verbosity_val = re.search('-V ?([01234])?', sys_args)
            if verbosity_val:
                pygtftk.utils.VERBOSITY = int(verbosity_val.group(1))
            else:
                pygtftk.utils.VERBOSITY = 0

        match = False

        if isinstance(self.file_ext, str):
            extension_list = [self.file_ext]
        else:
            extension_list = list(self.file_ext)

        for this_ext in extension_list:
            if re.search(ext2regexp[this_ext], string):
                match = True
                break

        if not match:
            message('Not a valid filename extension :' + string, type="WARNING")
            message('Extension expected: ' + ext2regexp[this_ext], type="ERROR")

now = datetime.datetime.now()

    if pygtftk.utils.VERBOSITY > 2:
        ho_min = str(now.hour) + ":" + str(now.minute).zfill(2) + ":" + str(now.second).zfill(2)
    else:
        ho_min = str(now.hour) + ":" + str(now.minute).zfill(2)

    do_it = False

    if type not in ["INFO", "ERROR", "WARNING", "DEBUG", "DEBUG_MEM"]:
        raise GTFtkError(
            "Type should be one of INFO, ERROR, WARNING, DEBUG, DEBUG_MEM.")

    if force:
        VERBOSITY_BACK = pygtftk.utils.VERBOSITY
        pygtftk.utils.VERBOSITY = 2

    if pygtftk.utils.VERBOSITY >= 2:
        do_it = True

    elif pygtftk.utils.VERBOSITY == 1:
        if type == "ERROR":
            do_it = True
        elif type == "WARNING":
            do_it = True
        elif type == "INFO":
            do_it = True
        elif type == "DEBUG_MEM":
            do_it = False
        elif type == "DEBUG":
            do_it = False

# -------------------------------------------------------------------------

    if ensembl_collection == 'vertebrate':

        host = "ftp.ensembl.org"
        user = "anonymous"  # votre identifiant
        password = "anonymous@gtftk.fr"
    elif ensembl_collection in ['protists', 'fungi', 'plants', 'metazoa']:

        host = "ftp.ensemblgenomes.org"
        user = "anonymous"
        password = "anonymous@gtftk.fr"

    try:
        ftp = ftputil.FTPHost(host, user, password)
        if pygtftk.utils.VERBOSITY:
            message("Connected to ensembl FTP website.")
    except FTPOSError as err:
        message(str(err))
        message("Unable to connect (FTPOSError).", type="ERROR")

    try:
        ftp.chdir('/pub')
        message("Successfully change directory to pub")
    except:
        message("Unable to change directory to 'pub'.",
                type="ERROR")

    if ensembl_collection in ['protists', 'fungi', 'plants', 'metazoa']:
        try:
            ftp.chdir(ensembl_collection)
            message("Successfully change directory to " + ensembl_collection)

# -------------------------------------------------------------------------
    # Compute coverage
    #
    # -------------------------------------------------------------------------

    result_bed = bw_cov_mp(bw_list=bw_list,
                           region_file=open(region_bed.name),
                           labels=labels,
                           bin_nb=nb_window,
                           pseudo_count=pseudo_count,
                           zero_to_na=zero_to_na,
                           nb_proc=nb_proc,
                           n_highest=n_highest,
                           stat=stat,
                           verbose=pygtftk.utils.VERBOSITY)

    if matrix_out:
        result_bed.close()

        df_first = pd.read_csv(result_bed.name, sep="\t", header=None)

        if int(re.sub("\..*", "", pd.__version__)) > 0:
            df_first = df_first.iloc[:, [0, 1, 2, 3, 5, 4]]
        else:
            df_first = df_first.ix[:, [0, 1, 2, 3, 5, 4]]

        df_list = []

        for i in range(len(labels)):
            # create a sub data frame containing the coverage values of the
            # current bwig

for key, value in list(args.items()):
                    if isinstance(value, io.IOBase):
                        value = value.name
                    else:
                        value = str(value)

                    cmd_ob.logger.info("Argument: " + key + "=" + value)

            # Set the level of verbosity
            # Can be None if -V is used without value
            # (nargs)
            if args['verbosity'] is None:
                pygtftk.utils.VERBOSITY = 1
            else:
                pygtftk.utils.VERBOSITY = int(args['verbosity'])

            # Set whether date should be added to
            # output file
            if args['no_date']:
                pygtftk.utils.ADD_DATE = False

            arg_list_to_del = ['bash_comp', 'add_chr', 'version', 'help',
                               'plugin_tests', 'list_plugins', 'plugin_tests_no_conn',
                               'r_libs', 'add_plugin', 'update_plugins', 'system_info',
                               'plugin_path', 'no_date', 'keep_all', 'logger_file',
                               'tmp_dir', 'verbosity', 'command', 'write_message_to_file']
            for cur_arg in arg_list_to_del:
                try:
                    del args[cur_arg]
                except KeyError:
                    pass

now = datetime.datetime.now()

    if pygtftk.utils.VERBOSITY > 2:
        ho_min = str(now.hour) + ":" + str(now.minute).zfill(2) + ":" + str(now.second).zfill(2)
    else:
        ho_min = str(now.hour) + ":" + str(now.minute).zfill(2)

    do_it = False

    if type not in ["INFO", "ERROR", "WARNING", "DEBUG", "DEBUG_MEM"]:
        raise GTFtkError(
            "Type should be one of INFO, ERROR, WARNING, DEBUG, DEBUG_MEM.")

    if force:
        VERBOSITY_BACK = pygtftk.utils.VERBOSITY
        pygtftk.utils.VERBOSITY = 2

    if pygtftk.utils.VERBOSITY >= 2:
        do_it = True

    elif pygtftk.utils.VERBOSITY == 1:
        if type == "ERROR":
            do_it = True
        elif type == "WARNING":
            do_it = True
        elif type == "INFO":
            do_it = True
        elif type == "DEBUG_MEM":
            do_it = False
        elif type == "DEBUG":
            do_it = False

suffix=".bed")

            dws_region_bo.saveas(dws_bed_file.name)

            tmp_file = bw_profile_mp(in_bed_file=dws_bed_file.name,
                                     nb_proc=nb_proc,
                                     big_wig=[
                                         x.name for x in bigwiglist],
                                     bin_nb=around_bin_nb,
                                     pseudo_count=pseudo_count,
                                     stranded=not no_stranded,
                                     type="downstream",
                                     labels=labels,
                                     outputfile=outputfile.name,
                                     zero_to_na=zero_to_na,
                                     verbose=pygtftk.utils.VERBOSITY)

            outputfile_list["downstream"] = tmp_file

    # -------------------------------------------------------------------------
    #
    # Merge file using pandas
    #
    # -------------------------------------------------------------------------

    message("Reading (pandas): " + outputfile_list["main"].name, type="DEBUG")
    df_main = pd.read_csv(outputfile_list["main"].name, sep="\t")
    # save strand and end
    # They will re-joined added later
    df_copy = df_main[['bwig', 'chrom', 'gene',
                       'strand', 'start', 'end']]