INNER CODE UNIT · Python
add_prokaryotic_fraction_parser
wwood/singlem · singlem/main.py:582
def add_prokaryotic_fraction_parser(name, description, deprecated=False):
parser_group = 'exclude' if name == "microbial_fraction" else 'Tools'
parser = bird_argparser.new_subparser(name, description, parser_group=parser_group)
read_fraction_io_args = parser.add_argument_group('input')
read_fraction_io_args.add_argument('-p', '--input-profile', help="Input taxonomic profile file [required]", required=True)
read_fraction_sequence_input_group1 = parser.add_argument_group('Read information [1+ args required]')
read_fraction_sequence_input_group = read_fraction_sequence_input_group1.add_mutually_exclusive_group(required=True)
# Keep parity of these arguments with the 'pipe' command
read_fraction_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. These must be the same ones that were used to generate the input profile.')
read_fraction_sequence_input_group1.add_argument('-2', '--reverse',
nargs='+',
metavar='sequence_file',
help='reverse reads to be searched. Can be FASTA or FASTQ format, GZIP-compressed or not. These must be the same reads that were used to generate the input profile.')
read_fraction_sequence_input_group.add_argument('--input-metagenome-sizes', help="TSV file with 'sample' and 'num_bases' as a header, where sample matches the input profile name, and num_reads is the total number (forward+reverse) of bases in the metagenome that was analysed with 'pipe'. These must be the same reads that were used to generate the input profile.")
read_fraction_database_args = parser.add_argument_group('database')