kaptive.cli

fmt_opts(opts)

Format opts shared by convert and extract

Source code in kaptive/cli.py

def fmt_opts(opts: argparse.ArgumentParser):
    """Format opts shared by convert and extract"""
    opts.add_argument('--fna', metavar='', nargs='?', default=None, const='.', type=check_out,
                      help='Convert to locus nucleotide sequences in fasta format\n'
                           'Accepts a single file or a directory (default: cwd)')
    opts.add_argument('--ffn', metavar='', nargs='?', default=None, const='.', type=check_out,
                      help='Convert to locus gene nucleotide sequences in fasta format\n'
                           'Accepts a single file or a directory (default: cwd)')
    opts.add_argument('--faa', metavar='', nargs='?', default=None, const='.', type=check_out,
                      help='Convert to locus gene protein sequences in fasta format\n'
                           'Accepts a single file or a directory (default: cwd)')

other_fmt_opts(opts)

Format opts shared by convert and assembly

Source code in kaptive/cli.py

def other_fmt_opts(opts: argparse.ArgumentParser):
    """Format opts shared by convert and assembly"""
    opts.add_argument('--no-header', action='store_true', help='Suppress header line')