Mastering Python for Bioinformatics by Ken Youens-Clark

Author:Ken Youens-Clark
Language: eng
Format: epub
Publisher: O'Reilly Media
Published: 2021-05-11T00:00:00+00:00

$ new.py -fp 'Find locations of N-glycosylation motif' mprt.py Done, see new script "mprt.py".

You should define a positional file argument and an optional download directory as the arguments to the program:

class Args(NamedTuple): """ Command-line arguments """ file: TextIO download_dir: str def get_args() -> Args: """Get command-line arguments""" parser = argparse.ArgumentParser( description='Find location of N-glycosylation motif', formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('file', help='Input text file of UniProt IDs', metavar='FILE', type=argparse.FileType('rt')) parser.add_argument('-d', '--download_dir', help='Directory for downloads', metavar='DIR', type=str, default='fasta') args = parser.parse_args() return Args(args.file, args.download_dir)

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