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search.py
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/
search.py
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"""search a signature against other signatures"""
from sourmash.cli.utils import add_ksize_arg, add_moltype_args
def subparser(subparsers):
subparser = subparsers.add_parser('search')
subparser.add_argument(
'query', help='query signature'
)
subparser.add_argument(
'databases', nargs='+',
help='signatures/SBTs to search',
)
subparser.add_argument(
'--traverse-directory', action='store_true',
help='search all signatures underneath directories'
)
subparser.add_argument(
'-q', '--quiet', action='store_true',
help='suppress non-error output'
)
subparser.add_argument(
'--threshold', metavar='T', default=0.08, type=float,
help='minimum threshold for reporting matches; default=0.08'
)
subparser.add_argument(
'--save-matches', metavar='FILE',
help='output matching signatures to the specified file'
)
subparser.add_argument(
'--best-only', action='store_true',
help='report only the best match (with greater speed)'
)
subparser.add_argument(
'-n', '--num-results', default=3, type=int, metavar='N',
help='number of results to report'
)
subparser.add_argument(
'--containment', action='store_true',
help='evaluate containment rather than similarity'
)
subparser.add_argument(
'--ignore-abundance', action='store_true',
help='do NOT use k-mer abundances if present; note: has no effect if '
'--containment is specified'
)
subparser.add_argument(
'--scaled', metavar='FLOAT', type=float, default=0,
help='downsample query to this scaled factor (yields greater speed)'
)
subparser.add_argument(
'-o', '--output', metavar='FILE',
help='output CSV containing matches to this file'
)
subparser.add_argument(
'--md5', default=None,
help='select the signature with this md5 as query'
)
add_ksize_arg(subparser, 31)
add_moltype_args(subparser)
def main(args):
import sourmash
return sourmash.commands.search(args)