def add_options(parser):
    """
    Add optional arguments to the parser
    """
    partial_action = common.partial_append_action
    file_mods = parser.add_argument_group("Sequence File Modification")
    file_mods.add_argument('--line-wrap', dest='line_wrap', metavar='N',
        type=int, help='Adjust line wrap for sequence strings.  '
        'When N is 0, all line breaks are removed. Only fasta files '
        'are supported for the output format.')
    file_mods.add_argument('--sort', dest='sort',
        choices=['length-asc', 'length-desc', 'name-asc', 'name-desc'],
        help='Perform sorting by length or name, ascending or descending. '
        'ASCII sorting is performed for names')

    parser.epilog = """Filters using regular expressions are case-sensitive
    by default. Append "(?i)" to a pattern to make it case-insensitive."""

    seq_mods = parser.add_argument_group("Sequence Modificaton")
    seq_mods.add_argument('--apply-function', type=module_function,
            metavar='/path/to/module.py:function_name[:parameter]',
            help="""Specify a custom function to apply to the input sequences,
            specified as /path/to/file.py:function_name. Function should accept
            an iterable of Bio.SeqRecord objects, and yield SeqRecords. If the
            parameter is specified, it will be passed as a string as the second
            argument to the function. Specify more than one to chain.""",
            default=[], action='append')
    seq_mods.add_argument('--cut', dest='transforms',
            metavar="start:end[,start2:end2]",
            type=common.sequence_slices,
            action=partial_action(transform.multi_cut_sequences, 'slices'),
            help="""Keep only the residues within the 1-indexed start and end
            positions specified, : separated. Includes last item. Start or end
            can be left unspecified to indicate start/end of sequence. A
            negative start may be provided to indicate an offset from the end
            of the sequence. Note that to prevent negative numbers being
            interpreted as flags, this should be written with an equals
            sign between `--cut` and the argument, e.g.: `--cut=-10:`""")
    seq_mods.add_argument('--relative-to', dest='cut_relative', metavar='ID',
            help="""Apply --cut relative to the indexes of non-gap residues in
            sequence identified by ID""")
    seq_mods.add_argument('--drop', dest='transforms',
            metavar='start:end[,start2:end2]',
            type=common.sequence_slices,
            action=partial_action(transform.drop_columns, 'slices'),
            help="""Remove the residues at the specified indices. Same format as `--cut`.""")
    seq_mods.add_argument('--dash-gap',
            action=partial_action(transform.dashes_cleanup), dest='transforms',
            help="""Replace any of the characters "?.:~" with a "-" for all
            sequences""")
    seq_mods.add_argument('--lower',
            action=partial_action(transform.lower_sequences),
            dest='transforms', help='Translate the sequences to lower case')
    seq_mods.add_argument('--mask', metavar="start1:end1[,start2:end2]",
            action=partial_action(transform.multi_mask_sequences, 'slices'),
            type=common.sequence_slices, dest='transforms', help="""Replace
            residues in 1-indexed slice with gap-characters. If --relative-to
            is also specified, coordinates are relative to the sequence ID
            provided.""")
    seq_mods.add_argument('--reverse',
            action=partial_action(transform.reverse_sequences),
            dest='transforms', help='Reverse the order of sites in sequences')
    seq_mods.add_argument('--reverse-complement', dest='transforms',
            action=partial_action(transform.reverse_complement_sequences),
            help='Convert sequences into reverse complements')
    seq_mods.add_argument('--squeeze', action=partial_action(transform.squeeze),
            dest='transforms',
            help='''Remove any gaps that are present in the same
            position across all sequences in an alignment (equivalent to
            --squeeze-threshold=1.0)''')
    seq_mods.add_argument('--squeeze-threshold', dest='transforms',
            action=partial_action(transform.squeeze, 'gap_threshold'),
            type=common.typed_range(float, 0.0, 1.0),
            metavar='PROP', help="""Trim columns from an alignment which
            have gaps in least the specified proportion of sequences.""")
    seq_mods.add_argument('--transcribe', dest='transforms',
            action=partial_action(transform.transcribe, 'transcribe'),
            choices=('dna2rna', 'rna2dna'), help="""Transcription and back
            transcription for generic DNA and RNA. Source sequences must be the
            correct alphabet or this action will likely produce incorrect
            results.""")
    seq_mods.add_argument('--translate', dest='transforms',
            action=partial_action(transform.translate, 'translate'),
            choices=['dna2protein', 'rna2protein', 'dna2proteinstop',
                'rna2proteinstop'], help="""Translate from generic DNA/RNA to
            proteins. Options with "stop" suffix will NOT translate through
            stop codons .  Source sequences must be the correct alphabet or
            this action will likely produce incorrect results.""")
    seq_mods.add_argument('--ungap',
            action=partial_action(transform.ungap_sequences),
            dest='transforms', help='Remove gaps in the sequence alignment')
    seq_mods.add_argument('--upper',
            action=partial_action(transform.upper_sequences),
            dest='transforms', help='Translate the sequences to upper case')

    seq_select = parser.add_argument_group("Record Selection")

    seq_select.add_argument('--deduplicate-sequences',
        action='store_const', const=None, default=False,
         dest='deduplicate_sequences', help='Remove any duplicate sequences '
         'by sequence content, keep the first instance seen')
    seq_select.add_argument('--deduplicated-sequences-file', action='store',
        metavar='FILE', dest='deduplicate_sequences', default=False,
        type=common.FileType('wt'),
        help='Write all of the deduplicated sequences to a file')
    seq_select.add_argument('--deduplicate-taxa',
            action=partial_action(transform.deduplicate_taxa),
            dest='transforms', help="""Remove any duplicate sequences by ID,
            keep the first instance seen""")
    seq_select.add_argument('--exclude-from-file', metavar='FILE',
            type=common.FileType('rt'), help="""Filter sequences, removing
            those sequence IDs in the specified file""", dest='transforms',
            action=partial_action(transform.exclude_from_file, 'handle'))
    seq_select.add_argument('--include-from-file', metavar='FILE',
            type=common.FileType('rt'), help="""Filter sequences, keeping only
            those sequence IDs in the specified file""", dest='transforms',
            action=partial_action(transform.include_from_file, 'handle'))
    seq_select.add_argument('--head', metavar='N', dest='transforms',
            action=partial_action(transform.head, 'head'), help="""Trim
            down to top N sequences. With the leading `-', print all but the last N sequences.""")
    seq_select.add_argument('--max-length', dest='transforms', metavar='N',
            action=partial_action(transform.max_length_discard, 'max_length'),
            type=int, help="""Discard any sequences beyond the specified
            maximum length.  This operation occurs *before* all length-changing
            options such as cut and squeeze.""")
    seq_select.add_argument('--min-length', dest='transforms', metavar='N',
            action=partial_action(transform.min_length_discard, 'min_length'),
            type=int, help="""Discard any sequences less than the specified
            minimum length.  This operation occurs *before* cut and squeeze.""")
    seq_select.add_argument('--min-ungapped-length', metavar='N',
            action=partial_action(transform.min_ungap_length_discard,
                'min_length'), type=int, help="""Discard any sequences less
                than the specified minimum length, excluding gaps. This
                operation occurs *before* cut and squeeze.""",
                dest='transforms')
    seq_select.add_argument('--pattern-include', metavar='REGEX',
            action=partial_action(transform.name_include, 'filter_regex'),
            dest='transforms', help="""Filter the sequences by regular
            expression in ID or description""")
    seq_select.add_argument('--pattern-exclude', metavar='REGEX',
            action=partial_action(transform.name_exclude, 'filter_regex'),
            dest='transforms', help="""Filter the sequences by regular
            expression in ID or description""")
    seq_select.add_argument('--prune-empty',
            action=partial_action(transform.prune_empty), dest='transforms',
            help="Prune sequences containing only gaps ('-')")
    seq_select.add_argument('--sample', metavar='N', dest='transforms', type=int,
            action=partial_action(transform.sample, 'k'),
            help = """ Select a random sampling of sequences """)
    seq_select.add_argument('--sample-seed', metavar='N', type=int,
            help = """Set random seed for sampling of sequences""")
    seq_select.add_argument('--seq-pattern-include', metavar='REGEX',
            action=partial_action(transform.seq_include, 'filter_regex'),
            dest='transforms', help="""Filter the sequences by regular
            expression in sequence""")
    seq_select.add_argument('--seq-pattern-exclude', metavar='REGEX',
            action=partial_action(transform.seq_exclude, 'filter_regex'),
            dest='transforms', help="""Filter the sequences by regular
            expression in sequence""")
    seq_select.add_argument('--tail', metavar='N', dest='transforms',
            action=partial_action(transform.tail, 'tail'),
        help="""Trim down to bottom N sequences.  Use +N to output sequences starting with the Nth.""")

    id_mods = parser.add_argument_group("Sequence ID Modification")
    id_mods.add_argument('--first-name',
            action=partial_action(transform.first_name_capture),
            dest='transforms', help='''Take only the first whitespace-delimited
            word as the name of the sequence''')
    id_mods.add_argument('--name-suffix', metavar='SUFFIX',
            action=partial_action(transform.name_append_suffix, 'suffix'),
            dest='transforms', help='Append a suffix to all IDs.')
    id_mods.add_argument('--name-prefix', metavar='PREFIX',
            action=partial_action(transform.name_insert_prefix, 'prefix'),
            dest='transforms', help="""Insert a prefix for all
            IDs.""")
    id_mods.add_argument('--pattern-replace', nargs=2,
            metavar=('search_pattern', 'replace_pattern'),
            action=partial_action(transform.name_replace, ('search_regex',
                'replace_pattern')),
            dest='transforms', help="""Replace regex pattern "search_pattern"
            with "replace_pattern" in sequence ID and description""")
    id_mods.add_argument('--strip-range', dest='transforms',
            action=partial_action(transform.strip_range), help="""Strip ranges
            from sequences IDs, matching </x-y>""")

    format_group = parser.add_argument_group('Format Options')
    format_group.add_argument('--input-format', metavar='FORMAT',
            help="Input file format (default: determine from extension)")
    format_group.add_argument('--output-format', metavar='FORMAT',
            help="Output file format (default: determine from extension)")

    parser.add_argument('--alphabet', choices=ALPHABETS,
            help="""Input alphabet. Required for writing NEXUS.""")

    return parser
Add optional arguments to the parser