How to use the pygtftk.utils function in pygtftk

exit(0)

        lang = cls.cmd_obj_list[cmd_name].lang

        if lang == 'Python':
            if args.tmp_dir is not None:

                if not os.path.exists(args.tmp_dir):
                    msg = "Creating directory {d}."
                    message(msg.format(d=args.tmp_dir), type="INFO")
                    mkdir_p(args.tmp_dir)
                if not os.path.isdir(args.tmp_dir):
                    msg = "{d} is not a directory."
                    message(msg.format(d=args.tmp_dir), type="ERROR")

                pygtftk.utils.TMP_DIR = args.tmp_dir

        return args

to write to a gtf file.

        :Example:

        >>> from pygtftk.utils import get_example_feature
        >>> from pygtftk.utils import TAB
        >>> feat = get_example_feature()
        >>> assert len(feat.format().split(TAB)) == 9

        """

        tok_list = list()
        for key, val in list(self.attr.items()):
            tok_list += [key + ' "' + val + '";']

        if pygtftk.utils.ADD_CHR == 1:
            chrom_out = 'chr' + self.chrom
        else:
            chrom_out = self.chrom

        token = [chrom_out,
                 self.src,
                 self.ft_type,
                 str(self.start),
                 str(self.end),
                 str(self.score),
                 self.strand,
                 str(self.frame),
                 ' '.join(tok_list)]

        return '\t'.join(token)

>>> from  pygtftk.utils import get_example_file
        >>> from pygtftk.gtf_interface import GTF
        >>> from pygtftk.utils import make_tmp_file
        >>> from pygtftk.utils import simple_line_count
        >>> from pygtftk.utils import simple_nb_column
        >>> a_file = get_example_file()[0]
        >>> a_tab = GTF(a_file).extract_data("transcript_id,gene_id")
        >>> out_file = make_tmp_file()
        >>> a_tab.write(out_file)
        >>> out_file.close()
        >>> assert simple_line_count(out_file) == 70
        >>> assert simple_nb_column(out_file) == 2
        """

        for i in self:
            pygtftk.utils.write_properly(sep.join(list(i)), outfile)

# .pyc -> .py
        fun_path = cmd_ob.fun.rstrip("c")
        tmp_module = SourceFileLoader('tmp_module', fun_path).load_module()
        fun = getattr(tmp_module, args['command'])

        # Save args to log file

        if cmd_ob.lang == "Python":

            # Add 'chr' to the chromosome names
            if args['add_chr']:
                pygtftk.utils.ADD_CHR = 1

            if args['write_message_to_file'] is not None:
                pygtftk.utils.MESSAGE_FILE = args['write_message_to_file']

            if args['logger_file'] is not None:
                if os.path.isdir(args['logger_file']):
                    message("ERROR --logger-file is a directory.",
                            type="ERROR")

                if not os.path.exists(args['logger_file']):
                    logger_file_h = open(args['logger_file'], 'w+')
                    logger_file_h.close()

                log_format = "-->> %(asctime)s - %(name)s - " + \
                             "%(levelname)s - %(message)s"
                datefmt = '%Y-%m-%d %H:%M:%S'

                logging.basicConfig(filename=args['logger_file'],
                                    level=logging.INFO,

self.start = val
        elif key == 'end':
            self.end = val
        elif key in ['src', 'source']:
            self.src = val
        elif key == 'score':
            self.score = val
        elif key == 'frame':
            self.frame = val
        else:
            if upon_none == 'continue':
                pass
            elif upon_none == 'set_na':
                self.add_attr(key, ".")
            elif upon_none == 'raise':
                pygtftk.utils.message('Attribute ' + key + ' does not exist',
                                      type="ERROR")
            else:
                pygtftk.utils.message('Attribute ' + key + ' does not exist',
                                      type="ERROR")

# Add a logger to the command object
        cls.cmd_obj_list[args['command']].logger = logging.getLogger(__name__)

        # .pyc -> .py
        fun_path = cmd_ob.fun.rstrip("c")
        tmp_module = SourceFileLoader('tmp_module', fun_path).load_module()
        fun = getattr(tmp_module, args['command'])

        # Save args to log file

        if cmd_ob.lang == "Python":

            # Add 'chr' to the chromosome names
            if args['add_chr']:
                pygtftk.utils.ADD_CHR = 1

            if args['write_message_to_file'] is not None:
                pygtftk.utils.MESSAGE_FILE = args['write_message_to_file']

            if args['logger_file'] is not None:
                if os.path.isdir(args['logger_file']):
                    message("ERROR --logger-file is a directory.",
                            type="ERROR")

                if not os.path.exists(args['logger_file']):
                    logger_file_h = open(args['logger_file'], 'w+')
                    logger_file_h.close()

                log_format = "-->> %(asctime)s - %(name)s - " + \
                             "%(levelname)s - %(message)s"
                datefmt = '%Y-%m-%d %H:%M:%S'

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

            # Run the command
            fun(**args)

        else:

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

    outputfile_list = {}
    message("Using %d bins for main region." % bin_nb)

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

    outputfile_list["main"] = tmp_file

    # -------------------------------------------------------------------------
    # If transcript was requested
    # we must process flanking regions
    # We need to retrieve coverage of promoter [-upstream, 0]
    # as transcript coverage window size will depend on transcript length.
    # For promoter the length of windows will be fixed.
    # -------------------------------------------------------------------------

    if ft_type in ['transcript', 'user_regions']:

        # Number of bins for TTS and TSS
        around_bin_nb = int(round(bin_nb * bin_around_frac))
        if around_bin_nb < 1:

del parser.__dict__['_option_string_actions']['-h']
        except:
            pass

        self.parser = parser
        self.fun = fun
        self.desc = desc
        self.logger = None
        self.lang = lang
        self.test = test
        self.rlib = rlib

        if re.search("@test", self.test):
            pygtftk.cmd_manager.CmdManager.add_command(self)
        else:
            pygtftk.utils.message(
                "%s command has no test and won't be installed." % name,
                type="WARNING")