/
__init__.py
35 lines (31 loc) · 1.17 KB
/
__init__.py
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"""Define the command line interface for sourmash lca
The top level CLI is defined in ../__init__.py. This module defines the CLI for
`sourmash lca` operations.
"""
from . import classify
from . import compare_csv
from . import gather
from . import index
from . import rankinfo
from . import summarize
from ..utils import command_list
from argparse import SUPPRESS, RawDescriptionHelpFormatter
import os
import sys
def subparser(subparsers):
subparser = subparsers.add_parser('lca', formatter_class=RawDescriptionHelpFormatter, usage=SUPPRESS)
desc = 'Operations\n'
clidir = os.path.dirname(__file__)
ops = command_list(clidir)
for subcmd in ops:
docstring = getattr(sys.modules[__name__], subcmd).__doc__
helpstring = 'sourmash lca {op:s} --help'.format(op=subcmd)
desc += ' {hs:33s} {ds:s}\n'.format(hs=helpstring, ds=docstring)
s = subparser.add_subparsers(
title='Taxonomic utilities', dest='subcmd', metavar='subcmd', help=SUPPRESS,
description=desc
)
for subcmd in ops:
getattr(sys.modules[__name__], subcmd).subparser(s)
subparser._action_groups.reverse()
subparser._optionals.title = 'Options'