/
prefetch.py
69 lines (63 loc) · 2.21 KB
/
prefetch.py
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"""search a signature against dbs, find all overlaps"""
from sourmash.cli.utils import (add_ksize_arg, add_moltype_args,
add_picklist_args, add_scaled_arg)
def subparser(subparsers):
subparser = subparsers.add_parser('prefetch')
subparser.add_argument('query', help='query signature')
subparser.add_argument("databases",
nargs="*",
help="one or more databases to search",
)
subparser.add_argument(
"--db-from-file",
default=None,
help="list of paths containing signatures to search"
)
subparser.add_argument(
"--linear", action='store_true',
help="force linear traversal of indexes to minimize loading time and memory use"
)
subparser.add_argument(
'--no-linear', dest="linear", action='store_false',
)
subparser.add_argument(
'-q', '--quiet', action='store_true',
help='suppress non-error output'
)
subparser.add_argument(
'-d', '--debug', action='store_true'
)
subparser.add_argument(
'-o', '--output', metavar='FILE',
help='output CSV containing matches to this file'
)
subparser.add_argument(
'--save-matches', metavar='FILE',
help='save all matching signatures from the databases to the '
'specified file or directory'
)
subparser.add_argument(
'--threshold-bp', metavar='REAL', type=float, default=5e4,
help='reporting threshold (in bp) for estimated overlap with remaining query hashes (default=50kb)'
)
subparser.add_argument(
'--save-unmatched-hashes', metavar='FILE',
help='output unmatched query hashes as a signature to the '
'specified file'
)
subparser.add_argument(
'--save-matching-hashes', metavar='FILE',
help='output matching query hashes as a signature to the '
'specified 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)
add_picklist_args(subparser)
add_scaled_arg(subparser, 0)
def main(args):
import sourmash
return sourmash.commands.prefetch(args)