How to use the pygtftk.arg_formatter.FormattedFile function in pygtftk

"""The program parser."""
    parser = argparse.ArgumentParser(add_help=True)

    parser_grp = parser.add_argument_group('Arguments')

    parser_grp.add_argument('-i', '--inputfile',
                            help="Path to the GTF file. Default to STDIN",
                            default=sys.stdin,
                            metavar="GTF",
                            type=arg_formatter.FormattedFile(mode='r', file_ext=('gtf', 'gtf.gz')))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="GTF/TXT",
                            type=arg_formatter.FormattedFile(mode='w', file_ext=('gtf', 'txt')))

    parser_grp.add_argument('-f', '--text-format',
                            help="Return a text format.",
                            action="store_true")

    parser_grp.add_argument('-a',
                            '--key-name',
                            type=str,
                            default="nb_tx",
                            help="If gtf format is requested, the name of the key.",
                            required=False)

    return parser

def make_parser():
    """The program parser."""
    parser = argparse.ArgumentParser(add_help=True)

    parser_grp = parser.add_argument_group('Arguments')

    parser_grp.add_argument('-i', '--inputfile',
                            help="Path to the GTF file. Default to STDIN",
                            default=sys.stdin,
                            metavar="GTF",
                            type=arg_formatter.FormattedFile(mode='r', file_ext=('gtf', 'gtf.gz')))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file (BED).",
                            default=sys.stdout,
                            metavar="BED",
                            type=arg_formatter.FormattedFile(mode='w', file_ext='bed'))

    parser_grp.add_argument('-b', '--by-transcript',
                            help="The intronic regions are returned for each"
                                 " transcript.",
                            action="store_true")

    parser_grp.add_argument('-n', '--names',
                            help="The key(s) that should be used as name (if -b is used).",
                            default="gene_id,transcript_id",
                            metavar="NAME",

parser = argparse.ArgumentParser(add_help=True)

    parser_grp = parser.add_argument_group('Arguments')

    parser_grp.add_argument('-i', '--inputfile',
                            help="Path to the GTF file. Default to STDIN.",
                            default=sys.stdin,
                            metavar="GTF",
                            required=False,
                            type=arg_formatter.FormattedFile(mode='r', file_ext=('gtf', 'gtf.gz')))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="TXT",
                            type=arg_formatter.FormattedFile(mode='w', file_ext='txt'))

    parser_grp.add_argument('-d', '--header',
                            help="A comma-separated list of string to use as header.",
                            default=None,
                            type=str,
                            required=False)

    parser_grp.add_argument('-t', '--additional-text',
                            help="A facultative text to be printed in the third "
                                 "column (e.g species name).",
                            default=None,
                            metavar="TEXT",
                            type=str,
                            required=False)

    return parser

"""parse"""
    parser = argparse.ArgumentParser(add_help=True)

    parser_grp = parser.add_argument_group('Argument')

    parser_grp.add_argument('-i', '--inputfile',
                            help="Path to the GTF file. Default to STDIN",
                            default=sys.stdin,
                            metavar="GTF",
                            type=arg_formatter.FormattedFile(mode='r', file_ext=('gtf', 'gtf.gz')))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="GTF",
                            type=arg_formatter.FormattedFile(mode='w', file_ext=('bed')))

    parser_grp.add_argument('-g', '--go-id',
                            help='The GO ID (e.g GO:0003700). Default is to return all genes.',
                            default=None,
                            type=str,
                            required=False)

    parser_grp.add_argument('-s', '--species',
                            help='The dataset/species. Use select_by_go to get the list of species',
                            default="hsapiens",
                            type=str,
                            required=False)

    parser_grp.add_argument('-u', '--upstream',
                            help="Extend the TSS in 5' by a given value.",
                            default=5000,

def make_parser():
    """The program parser."""
    parser = argparse.ArgumentParser(add_help=True)

    parser_grp = parser.add_argument_group('Arguments')

    parser_grp.add_argument('-i', '--inputfile',
                            help="Path to the GTF file. Default to STDIN",
                            default=sys.stdin,
                            metavar="GTF",
                            type=arg_formatter.FormattedFile(mode='r', file_ext=('gtf', 'gtf.gz')))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output FASTA file.",
                            default=sys.stdout,
                            metavar="FASTA",
                            type=arg_formatter.FormattedFile(mode='w', file_ext='fasta'))

    parser_grp.add_argument('-g', '--genome',
                            help="The genome in fasta format. Accept path with wildcards (e.g. *.fa).",
                            default=None,
                            metavar="FASTA",
                            action=globbedFileList,
                            required=True)

    parser_grp.add_argument('-w', '--with-introns',
                            help="Set to true to include intronic regions.",

def make_parser():
    """The parser."""
    parser = argparse.ArgumentParser(add_help=True)

    parser_grp = parser.add_argument_group('Arguments')

    parser_grp.add_argument('-i', '--inputfile',
                            help="Path to the GTF file. Default to STDIN",
                            default=sys.stdin,
                            metavar="GTF",
                            type=arg_formatter.FormattedFile(mode='r', file_ext=('gtf', 'gtf.gz')))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="TXT",
                            type=arg_formatter.FormattedFile(mode='w', file_ext='txt'))

    parser_grp.add_argument('-s', '--separator',
                            help="The separator to be used for separating key names.",
                            default="\n",
                            metavar="SEP",
                            type=str)

    return parser

def make_parser():
    """The program parser."""
    parser = argparse.ArgumentParser(add_help=True)

    parser.add_argument('-i', '--inputfile',
                        help="Path to the GTF file. Default to STDIN",
                        default=sys.stdin,
                        metavar="GTF",
                        type=arg_formatter.FormattedFile(mode='r', file_ext=('gtf', 'gtf.gz')))

    parser.add_argument('-o', '--outputfile',
                        help="Output file.",
                        default=sys.stdout,
                        metavar="GTF",
                        type=arg_formatter.FormattedFile(mode='w', file_ext=('gtf')))

    return parser

def make_parser():
    """The program parser."""
    parser = argparse.ArgumentParser(add_help=True)

    parser.add_argument('-i', '--inputfile',
                        help="Path to the GTF file. Default to STDIN",
                        default=sys.stdin,
                        metavar="GTF",
                        type=arg_formatter.FormattedFile(mode='r', file_ext=('gtf', 'gtf.gz')))

    parser.add_argument('-o', '--outputfile',
                        help="Output file.",
                        default=sys.stdout,
                        metavar="GTF",
                        type=arg_formatter.FormattedFile(mode='w', file_ext=('gtf')))

    parser.add_argument('-k', '--key',
                        help='The key name',
                        default="chrom",
                        metavar="KEY",
                        type=str)

    parser.add_argument('-r', '--regexp',
                        help='The regular expression.',
                        default="^chr[0-9XY]+$",
                        type=str)

    parser.add_argument('-n', '--invert-match',
                        help='Not/invert match. Selected lines whose requested key '
                             'do not match the regexp.',
                        action="store_true")

def make_parser():
    """The program parser."""
    parser = argparse.ArgumentParser(add_help=True)

    parser_grp = parser.add_argument_group('Arguments')

    parser_grp.add_argument('-i', '--inputfile',
                            help="Path to the GTF file. Default to STDIN",
                            default=sys.stdin,
                            metavar="GTF",
                            type=arg_formatter.FormattedFile(mode='r', file_ext=('gtf', 'gtf.gz')))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="TXT/GTF",
                            type=arg_formatter.FormattedFile(mode='w', file_ext=('gtf', 'txt')))

    parser_grp.add_argument('-f', '--text-format',
                            help="Return a text format.",
                            action="store_true")

    parser_grp.add_argument('-a',
                            '--key-name',
                            type=str,
                            default="nb_exons",
                            help="The name of the key.",

def make_parser():
    """The parser."""
    parser = argparse.ArgumentParser(add_help=True)

    parser_grp = parser.add_argument_group('Arguments')

    parser_grp.add_argument('-i', '--inputfile',
                            help="Path to the GTF file. Default to STDIN.",
                            default=sys.stdin,
                            metavar="GTF",
                            required=False,
                            type=arg_formatter.FormattedFile(mode='r', file_ext=('gtf', 'gtf.gz')))

    parser_grp.add_argument('-o', '--outputfile',
                            help="Output file.",
                            default=sys.stdout,
                            metavar="TXT",
                            type=arg_formatter.FormattedFile(mode='w', file_ext='txt'))

    parser_grp.add_argument('-k', '--keys',
                            default="*",
                            help="The set of keys of interest.",
                            type=str,
                            required=False)

    parser_grp.add_argument('-t', '--additional-text',
                            help="A facultative text to be printed in the third "
                                 "column (e.g species name).",