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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)