/
watch.py
36 lines (32 loc) · 1.15 KB
/
watch.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
"""classify a stream of sequences"""
from sourmash.cli.utils import add_ksize_arg, add_moltype_args, add_num_arg
def subparser(subparsers):
subparser = subparsers.add_parser('watch')
subparser.add_argument('sbt_name', help='name of SBT to search')
subparser.add_argument('inp_file', nargs='?', default='/dev/stdin')
subparser.add_argument(
'-q', '--quiet', action='store_true',
help='suppress non-error output'
)
subparser.add_argument(
'-o', '--output',
help='save signature generated from data here'
)
subparser.add_argument(
'--threshold', metavar='T', default=0.05, type=float,
help='minimum threshold for matches (default=0.05)'
)
subparser.add_argument(
'--input-is-protein', action='store_true',
help='Consume protein sequences - no translation needed'
)
add_moltype_args(subparser)
subparser.add_argument(
'--name', type=str, default='stdin',
help='name to use for generated signature'
)
add_ksize_arg(subparser)
add_num_arg(subparser, 500)
def main(args):
import sourmash
return sourmash.commands.watch(args)