Harrison Deng
41c05cc521
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Added default MLST scheme Added multiple ways of defining a MLST scheme CSV output now shows database name for each scheme ID Now uses native argparse library for ensuring mutual exclusivity of arguments and whether or not one is required. Updated to use 0.13.* of engine
42 lines
1.3 KiB
Python
42 lines
1.3 KiB
Python
import argparse
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from importlib import metadata
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from os import path
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import os
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from autobigs.cli import info, st
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from autobigs.cli.meta import get_module_base_name
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import importlib
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root_parser = argparse.ArgumentParser(epilog='Use "%(prog)s info -h" to learn how to get available MLST databases, and their available schemes.'
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+ ' Once that is done, use "%(prog)s st -h" to learn how to retrieve MLST profiles.'
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)
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subparsers = root_parser.add_subparsers(required=False)
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info.setup_parser(subparsers.add_parser(get_module_base_name(info.__name__)))
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st.setup_parser(subparsers.add_parser(get_module_base_name(st.__name__)))
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root_parser.add_argument(
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"--version",
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action="store_true",
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default=False,
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required=False,
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help="Displays the autoBIGS.cli version, and the autoBIGS.Engine version."
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)
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def run():
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args = root_parser.parse_args()
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if args.version:
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print(f'autoBIGS.cli is running version {
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metadata.version("autobigs-cli")}.')
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print(f'autoBIGS.engine is running version {
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metadata.version("autobigs-engine")}.')
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if hasattr(args, "run"):
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args.run(args)
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elif not args.version:
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root_parser.print_usage()
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if __name__ == "__main__":
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run()
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