/
filter.py
41 lines (35 loc) · 1.19 KB
/
filter.py
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"""filter k-mers on abundance"""
import sys
from sourmash.cli.utils import add_moltype_args, add_ksize_arg
def subparser(subparsers):
subparser = subparsers.add_parser('filter')
subparser.add_argument('signatures', nargs='+')
subparser.add_argument(
'-q', '--quiet', action='store_true',
help='suppress non-error output'
)
subparser.add_argument(
'-o', '--output', metavar='FILE',
help='output signature to this file (default stdout)'
)
subparser.add_argument(
'--md5', type=str, default=None,
help='select signatures whose md5 contains this substring'
)
subparser.add_argument(
'--name', type=str, default=None,
help='select signatures whose name contains this substring'
)
subparser.add_argument(
'-m', '--min-abundance', type=int, default=1,
help='keep hashes >= this minimum abundance'
)
subparser.add_argument(
'-M', '--max-abundance', type=int, default=None,
help='keep hashes <= this maximum abundance'
)
add_ksize_arg(subparser, 31)
add_moltype_args(subparser)
def main(args):
import sourmash
return sourmash.sig.__main__.filter(args)