/
multigather.py
45 lines (40 loc) · 1.39 KB
/
multigather.py
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"'sourmash multigather' - gather many signatures against multiple databases."
from sourmash.cli.utils import add_ksize_arg, add_moltype_args
def subparser(subparsers):
subparser = subparsers.add_parser('multigather')
subparser.add_argument(
'--query', nargs='+', action='append',
help='query signature'
)
subparser.add_argument(
'--db', nargs='+', action='append',
help='signatures/SBTs to search',
)
subparser.add_argument(
'-q', '--quiet', action='store_true',
help='suppress non-error output'
)
subparser.add_argument(
'-d', '--debug', action='store_true'
)
subparser.add_argument(
'--traverse-directory', action='store_true',
help='search all signatures underneath directories'
)
subparser.add_argument(
'--threshold-bp', metavar='REAL', type=float, default=5e4,
help='threshold (in bp) for reporting results (default=50,000)'
)
subparser.add_argument(
'--scaled', metavar='FLOAT', type=float, default=0,
help='downsample query to the specified scaled factor'
)
subparser.add_argument(
'--ignore-abundance', action='store_true',
help='do NOT use k-mer abundances if present'
)
add_ksize_arg(subparser, 31)
add_moltype_args(subparser)
def main(args):
import sourmash
return sourmash.commands.multigather(args)