# -*- coding: utf-8 -*-
# (c) The James Hutton Institute 2017-2019
# (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) 2017-2019 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
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
"""Module providing command-line parser definitions."""
import sys
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter, Namespace
from typing import List, Optional
from pyani.scripts.parsers import (
download_parser,
index_parser,
createdb_parser,
anim_parser,
anib_parser,
aniblastall_parser,
fastani_parser,
report_parser,
plot_parser,
classify_parser,
scheduling_parser,
common_parser,
run_common_parser,
listdeps_parser,
)
# Process command-line
[docs]def parse_cmdline(argv: Optional[List] = None) -> Namespace:
"""
Parse command-line arguments for script.
:param argv: Namespace, command-line arguments
The script offers a single main parser, with subcommands for the actions:
- download
download all available NCBI assemblies below the passed taxonomy ID
- index
index genome sequence files in a subdirectory, for analysis
- createdb
generate SQLite database for data and analysis results
- anim
conduct ANIm analysis
- anib
conduct ANIb analysis
- aniblastall
conduct ANIblastall analysis
- fastani
conduct fastANI analysis
- report
generate output describing analyses, genomes, and results
- plot
generate graphical output describing results
- classify
produce graph-based classification of genomes on the basis of ANI analysis
"""
# Main parent parser
parser_main = ArgumentParser(
prog="pyani", formatter_class=ArgumentDefaultsHelpFormatter
)
subparsers = parser_main.add_subparsers(
title="subcommands", description="valid subcommands", help="additional help"
)
parser_main.add_argument(
"--version",
action="store_true",
default=False,
)
parser_main.add_argument(
"--citation",
action="store_true",
dest="citation",
default=False,
help="Display pyani citation",
)
# Parsers common to multiple subcommand parsers
parser_common = common_parser.build()
parser_scheduler = scheduling_parser.build()
parser_run_common = run_common_parser.build()
# Add subcommand parsers
download_parser.build(subparsers, parents=[parser_common])
index_parser.build(subparsers, parents=[parser_common])
createdb_parser.build(subparsers, parents=[parser_common])
anim_parser.build(
subparsers, parents=[parser_common, parser_scheduler, parser_run_common]
)
anib_parser.build(
subparsers, parents=[parser_common, parser_scheduler, parser_run_common]
)
aniblastall_parser.build(
subparsers, parents=[parser_common, parser_scheduler, parser_run_common]
)
fastani_parser.build(
subparsers, parents=[parser_common, parser_scheduler, parser_run_common]
)
report_parser.build(subparsers, parents=[parser_common])
plot_parser.build(subparsers, parents=[parser_common])
classify_parser.build(subparsers, parents=[parser_common])
listdeps_parser.build(subparsers, parents=[parser_common])
# Parse arguments
# The list comprehension is to allow PosixPaths to be defined and passed in testing
if argv is None:
if len(sys.argv) == 1:
argv = ["-h"]
else:
argv = sys.argv[1:]
return parser_main.parse_args([str(_) for _ in argv])