def register(parser):
add_output(parser)
add_nexus(parser)
parser.add_argument(
"-d",
"--deltree",
default=[],
type=list_of_ranges,
help=
"Remove the trees specified as comma-separated ranges of 1-based indices, "
"e.g. '1', '1-5', '1,20-30'")
parser.add_argument("-r",
"--resample",
type=int,
default=0,
help="Resample the trees every Nth tree")
parser.add_argument("-n",
"--random",
type=int,
default=0,
help="Randomly sample N trees from the treefile")
add_random_seed(parser)
parser.add_argument("-c",
"--removecomments",
action="store_true",
default=False,
help="Remove comments from the trees")
parser.add_argument("-t",
"--detranslate",
action="store_true",
default=False,
help="Remove taxa translation block from the trees")
def register(parser):
add_output(parser)
add_nexus(parser)
parser.add_argument("-n",
"--number",
action="store_true",
default=False,
help="Count the number of characters")
parser.add_argument("-c",
"--constant",
action="store_true",
default=False,
help="Remove the constant characters")
parser.add_argument("-u",
"--unique",
action="store_true",
default=False,
help="Remove the unique characters")
parser.add_argument(
"-x",
"--remove",
type=list_of_ranges,
help=
"Remove characters specified as comma-separated ranges of 1-based indices, "
"e.g. '1', '1-5', '1,20-30'")
parser.add_argument("-z",
"--zeros",
action="store_true",
default=False,
help="Remove the zero characters")
parser.add_argument("-s",
"--stats",
action="store_true",
default=False,
help="Print character-by-character stats")
def register(parser):
add_nexus(parser)
add_output(parser)
parser.add_argument("-n",
"--numchars",
default=0,
type=int,
help="Number of Characters to Generate")
def register(parser):
add_nexus(parser)
parser.add_argument(
'-t', '--type',
help='Typeof tally to compute',
choices=list(TALLY_TYPES.keys()),
default=list(TALLY_TYPES.keys())[0]
)
def register(parser):
add_nexus(parser)
parser.add_argument('-e',
"--extra",
help="add extra checks",
action='store_true')
parser.add_argument('-a',
"--ascertainment",
help="add ascertainment checks",
action='store_true')
def register(parser):
parser.add_argument('--charblock',
help=argparse.SUPPRESS,
action='store_false',
default=True)
parser.add_argument('--interleave',
help=argparse.SUPPRESS,
action='store_true',
default=False)
add_output(parser)
add_nexus(parser, many=True)
def register(parser):
parser.add_argument('site_index', help="Character index")
add_nexus(parser)
def register(parser):
add_output(parser)
add_nexus(parser)
def register(parser):
add_output(parser)
add_nexus(parser, many=True)
def register(parser):
add_nexus(parser)
add_format(parser, default='simple')