INNER CODE UNIT · Python
add_common_pipe_arguments
wwood/singlem · singlem/main.py:68
def add_common_pipe_arguments(argument_group, extra_args=False):
if extra_args:
sequence_input_group = argument_group.add_mutually_exclusive_group(required=True)
# Keep parity of these arguments with the 'read_fraction' command
sequence_input_group.add_argument('-1','--forward','--reads','--sequences',
nargs='+',
metavar='sequence_file',
help='nucleotide read sequence(s) (forward or unpaired) to be searched. Can be FASTA or FASTQ format, GZIP-compressed or not, short or long (but Nanopore >=10.4.1 or PacBio HiFi reads recommended).')
argument_group.add_argument('-2', '--reverse',
nargs='+',
metavar='sequence_file',
help='reverse reads to be searched. Can be FASTA or FASTQ format, GZIP-compressed or not.')
sequence_input_group.add_argument('-f', '--genome-fasta-files',
nargs='+',
metavar='PATH',
help='Path(s) to genome FASTA files. These are processed like input given with --forward, but use higher default values for --min-taxon-coverage and --min-orf-length.')
sequence_input_group.add_argument('-d', '--genome-fasta-directory',
metavar='PATH',