# -*- 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 download subcommand."""
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, _SubParsersAction
from pathlib import Path
from typing import List, Optional
from pyani.scripts import subcommands
# Subcommand parsers
[docs]def build(
subps: _SubParsersAction, parents: Optional[List[ArgumentParser]] = None
) -> None:
"""Return a command-line parser for the download subcommand.
:param subps: ArgumentParser.subparser
:param parents: additional Parser objects
The download subcommand takes specific arguments:
-t, --taxon (NCBI taxonomy IDs - comma-separated list, or one ID)
--email (email for providing to Entrez services)
--api_key (path to file containing personal API key for Entrez)
--retries (number of Entrez retry attempts to make)
--batchsize (number of Entrez records to download in a batch)
--timeout (how long to wait for Entrez query timeout)
-f, --force (allow existing directory overwrite)
--noclobber (don't replace existing files)
--labels (path to write labels file)
--classes (path to write classes file)
"""
parser = subps.add_parser(
"download", parents=parents, formatter_class=ArgumentDefaultsHelpFormatter
)
# Required argument: output directory
parser.add_argument(
"-o",
"--outdir",
action="store",
dest="outdir",
default=None,
type=Path,
help="output directory",
required=True,
)
# Required arguments for NCBI query
parser.add_argument(
"-t",
"--taxon",
dest="taxon",
action="store",
default=None,
help="NCBI taxonomy IDs (required, " + "comma-separated list)",
required=True,
)
parser.add_argument(
"--email",
dest="email",
action="store",
default=None,
help="Email associated with NCBI queries (required)",
required=True,
)
# Optional argument for faster/more robust NCBI query
parser.add_argument(
"--api_key",
dest="api_keypath",
action="store",
default="~/.ncbi/api_key",
type=Path,
help="Path to NCBI Entrez API key file",
)
# Arguments controlling connection to NCBI for download
parser.add_argument(
"--retries",
dest="retries",
action="store",
default=20,
help="Number of Entrez retry attempts per request",
)
parser.add_argument(
"--batchsize",
dest="batchsize",
action="store",
default=10000,
help="Entrez record return batch size",
)
parser.add_argument(
"--timeout",
dest="timeout",
type=int,
action="store",
default=10,
help="Timeout for URL connection (s)",
)
# Arguments controlling local filehandling
parser.add_argument(
"-f",
"--force",
dest="force",
action="store_true",
default=False,
help="Allow download to existing directory",
)
parser.add_argument(
"--noclobber",
dest="noclobber",
action="store_true",
default=False,
help="Don't replace existing files",
)
# Names for output files
parser.add_argument(
"--labels",
dest="labelfname",
action="store",
default="labels.txt",
help="Filename for labels file",
)
parser.add_argument(
"--classes",
dest="classfname",
action="store",
default="classes.txt",
help="Filename for classes file",
)
# Output for Kraken
parser.add_argument(
"--kraken",
dest="kraken",
action="store_true",
default=False,
help="Modify downloaded sequence ID for Kraken",
)
# Dry-run: do everything except download
parser.add_argument(
"--dry-run",
dest="dryrun",
action="store_true",
default=False,
help="Dry run only, do not download or overwrite.",
)
parser.set_defaults(func=subcommands.subcmd_download)