# -*- coding: utf-8 -*-
# (c) The James Hutton Institute 2016-2019
# (c) University of Strathclyde 2019-2020
# Author: Leighton Pritchard
#
# Contact:
# leighton.pritchard@strath.ac.uk
#
# Leighton Pritchard,
# Strathclyde Institute for Pharmacy and Biomedical Sciences,
# Cathedral Street,
# Glasgow,
# G4 0RE
# Scotland,
# UK
#
# The MIT License
#
# Copyright (c) 2016-2019 The James Hutton Institute
# Copyright (c) 2019-2020 University of Strathclyde
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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# THE SOFTWARE.
"""Provides parser for anim subcommand."""
import sys
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, _SubParsersAction
from pathlib import Path
from typing import List, Optional
from pyani import pyani_config
from pyani.scripts import subcommands
from pyani import __version__
[docs]def build(
subps: _SubParsersAction, parents: Optional[List[ArgumentParser]] = None
) -> None:
"""Return a command-line parser for the anim subcommand.
:param subps: collection of subparsers in main parser
:param parents: parsers from which arguments are inherited
"""
parser = subps.add_parser(
"anim", parents=parents, formatter_class=ArgumentDefaultsHelpFormatter
)
# Required arguments: input and output directories
parser.add_argument(
"-i",
"--indir",
action="store",
dest="indir",
default=None,
type=Path,
help="input genome directory",
required=True,
)
parser.add_argument(
"-o",
"--outdir",
action="store",
dest="outdir",
default=None,
type=Path,
help="output analysis results directory",
required=True,
)
# Optional arguments
parser.add_argument(
"--dbpath",
action="store",
dest="dbpath",
default=Path(".pyani/pyanidb"),
type=Path,
help="path to pyani database",
)
parser.add_argument(
"--nucmer_exe",
dest="nucmer_exe",
action="store",
default=pyani_config.NUCMER_DEFAULT,
type=Path,
help="path to NUCmer executable",
)
parser.add_argument(
"--filter_exe",
dest="filter_exe",
action="store",
default=pyani_config.FILTER_DEFAULT,
type=Path,
help="path to delta-filter executable",
)
parser.add_argument(
"--maxmatch",
dest="maxmatch",
action="store_true",
default=False,
help="override MUMmer to allow all NUCmer matches",
)
parser.add_argument(
"--nofilter",
dest="nofilter",
action="store_true",
default=False,
help="do not use delta-filter for 1:1 NUCmer matches",
)
parser.set_defaults(func=subcommands.subcmd_anim)