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categorize.py
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categorize.py
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"'sourmash categorize' - query an SBT for bes match, with many signatures."
import argparse
from sourmash.cli.utils import add_ksize_arg, add_moltype_args
def subparser(subparsers):
subparser = subparsers.add_parser('categorize')
subparser.add_argument('sbt_name', help='name of SBT to load')
subparser.add_argument(
'queries', nargs='+',
help='list of signatures to categorize'
)
subparser.add_argument(
'-q', '--quiet', action='store_true',
help='suppress non-error output'
)
add_ksize_arg(subparser, 31)
subparser.add_argument(
'--threshold', default=0.08, type=float,
help='minimum threshold for reporting matches; default=0.08'
)
subparser.add_argument('--traverse-directory', action="store_true")
subparser.add_argument(
'--ignore-abundance', action='store_true',
help='do NOT use k-mer abundances if present'
)
add_moltype_args(subparser)
# TODO: help messages in these
subparser.add_argument('--csv', help='output summary CSV to this file')
subparser.add_argument('--load-csv', default=None)
def main(args):
import sourmash
return sourmash.commands.categorize(args)