# -*- 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 classify subcommand."""
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, _SubParsersAction
from pathlib import Path
from typing import List, Optional
from pyani.scripts import subcommands
[docs]def build(
subps: _SubParsersAction, parents: Optional[List[ArgumentParser]] = None
) -> None:
"""Return a command-line parser for the classify subcommand.
:param subps: collection of subparsers in main parser
:param parents: parsers from which arguments are inherited
The classify subcommand takes specific arguments:
--cov_min (minimum coverage threshold for an edge)
--id_min (minimum identity threshold for an edge)
--resolution (number of identity thresholds to test)
"""
parser = subps.add_parser(
"classify", parents=parents, formatter_class=ArgumentDefaultsHelpFormatter
)
# Required arguments: output directory and run ID
parser.add_argument(
"-o",
"--outdir",
action="store",
dest="outdir",
default=None,
type=Path,
help="output directory",
required=True,
)
parser.add_argument(
"--run_id",
action="store",
dest="run_id",
default=None,
help="run ID to classify",
required=True,
)
# Optional arguments
parser.add_argument(
"--dbpath",
action="store",
dest="dbpath",
default=Path(".pyani/pyanidb"),
type=Path,
help="path to pyani database",
)
# Parameters for classification: minimum %coverage, %identity,
# and the resolution of thresholds to test
parser.add_argument(
"--cov_min",
dest="cov_min",
action="store",
type=float,
default=0.5,
help="minimum %%coverage for an edge",
)
parser.add_argument(
"--id_min",
dest="id_min",
action="store",
type=float,
default=0.8,
help="minimum %%identity for an edge",
)
parser.add_argument(
"--min_id",
dest="min_id",
action="store",
type=float,
default=None,
help="minimum identity threshold to test",
)
parser.add_argument(
"--max_id",
dest="max_id",
action="store",
type=float,
default=None,
help="maximum identity threshold to test",
)
parser.add_argument(
"--resolution",
dest="resolution",
action="store",
type=float,
default=1e-4,
help="number of identity thresholds to test",
)
parser.add_argument(
"--show_all",
dest="show_all",
action="store_true",
default=False,
help=(
"report all intervals in log (default: "
"only intervals where all subgraphs are k-complete"
),
)
parser.set_defaults(func=subcommands.subcmd_classify)