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#!/usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
# Copyright (C) 2015, Michigan State University.
# Copyright (C) 2015, The Regents of the University of California.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of the Michigan State University nor the names
# of its contributors may be used to endorse or promote products
# derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# Contact: khmer-project@idyll.org
"""Single entry point script for khmer."""
import argparse
import sys
import textwrap
from khmer.khmer_args import build_nodegraph_args
from oxli import build_graph
def get_parser():
"""Return the parser object for the oxli subcommand handler."""
parser = argparse.ArgumentParser(
description='Single entry point script for khmer',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
subparsers = parser.add_subparsers()
# build-graph (formerly load-graph.py) parsers here
parser_build_graph = \
subparsers.add_parser(
name='build-graph',
help="Load sequences into the compressible graph format "
"plus optional tagset")
parser_build_graph = build_nodegraph_args(parser=parser_build_graph)
build_graph.build_parser(parser_build_graph)
parser_build_graph.set_defaults(func=build_graph.main)
return parser
def main():
"""Parse the command line and kick off the subcommand."""
if len(sys.argv) < 2:
args = get_parser().parse_args(['--help'])
else:
args = get_parser().parse_args()
args.func(args)
if __name__ == '__main__':
main()