Python main Examples

Example #1

File: load-graph.py Project: zhaijj/khmer

#
# Contact: [email protected]
# pylint disable=missing-docstring
"""
Build a graph from the given sequences, save in <ptname>.

% python scripts/load-graph.py <ptname> <data1> [ <data2> <...> ]

Use '-h' for parameter help.
"""

import sys

from khmer.khmer_args import build_nodegraph_args
from oxli import build_graph


def get_parser():
    parser = build_nodegraph_args(descr="Load sequences into the compressible "
                                  "graph format plus optional tagset.",
                                  citations=['graph', 'SeqAn'])

    parser = build_graph.build_parser(parser)
    return parser


if __name__ == '__main__':
    build_graph.main(get_parser().parse_args())

# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:

Example #2

Use '-h' for parameter help.
"""

import sys
import threading

import khmer
from khmer.khmer_args import build_hashbits_args
from khmer.khmer_args import (report_on_config, info, add_threading_args)
from khmer.kfile import check_input_files, check_space
from khmer.kfile import check_space_for_hashtable
from oxli import build_graph


def get_parser():
    parser = build_hashbits_args(descr="Load sequences into the compressible "
                                 "graph format plus optional tagset.")

    parser = build_graph.build_parser(parser)
    return parser


if __name__ == '__main__':
    parser = get_parser()
    args = parser.parse_args()
    build_graph.main(args)
    sys.exit(0)

# vim: set ft=python ts=4 sts=4 sw=4 et tw=79:

Example #3

File: load-graph.py Project: Koteko/khmer

Use '-h' for parameter help.
"""
from __future__ import print_function, unicode_literals

import sys
import threading

import khmer
from khmer.khmer_args import build_hashbits_args
from khmer.khmer_args import (report_on_config, info, add_threading_args)
from khmer.kfile import check_input_files, check_space
from khmer.kfile import check_space_for_hashtable
from oxli import build_graph


def get_parser():
    parser = build_hashbits_args(descr="Load sequences into the compressible "
                                       "graph format plus optional tagset.")

    parser = build_graph.build_parser(parser)
    return parser


if __name__ == '__main__':
    parser = get_parser()
    args = parser.parse_args()
    build_graph.main(args)
    sys.exit(0)

# vim: set ft=python ts=4 sts=4 sw=4 et tw=79: