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summarize.py
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summarize.py
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"""summarize mixture"""
def subparser(subparsers):
subparser = subparsers.add_parser('summarize')
subparser.add_argument('--db', nargs='+', action='append',
help='one or more LCA databases to use')
subparser.add_argument('--query', nargs='*', default=[], action='append',
help='one or more signature files to use as queries')
subparser.add_argument('--query-from-file',
help='file containing list of signature files to query')
subparser.add_argument('--threshold', metavar='T', type=int, default=5,
help='minimum number of hashes to require for a match')
subparser.add_argument(
'-o', '--output', metavar='FILE',
help='file to which CSV output will be written'
)
subparser.add_argument('--scaled', metavar='FLOAT', type=float,
help='scaled value to downsample to')
subparser.add_argument('--ignore-abundance', action='store_true',
help='ignore hash abundances in query signatures do not weight results')
subparser.add_argument(
'-q', '--quiet', action='store_true',
help='suppress non-error output'
)
subparser.add_argument(
'-d', '--debug', action='store_true',
help='output debugging output'
)
def main(args):
import sourmash
return sourmash.lca.command_summarize.summarize_main(args)