<commit_before>#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
(c) 2014 <NAME> || http://faircloth-lab.org/
All rights reserved.

This code is distributed under a 3-clause BSD license. Please see
LICENSE.txt for more information.

Created on 31 January 2014 11:38 PST (-0800)
"""

from __future__ import absolute_import
#import os
import argparse
from curb import core


def get_args():
    parser = argparse.ArgumentParser(
        description="Run constraint tests using RAxML",
        formatter_class=argparse.ArgumentDefaultsHelpFormatter
    )
    parser.add_argument(
        '--config',
        required=True,
        help='Path to a YAML config file with constraint info.',
        action=core.FullPaths
    )
    parser.add_argument(
        '--alignments',
        required=True,
        help='A directory of PHYLIP alignments to use for tree inference.',
        action=core.FullPaths,
        type=core.is_dir
    )
    '''
    parser.add_argument(
        '--alignments',
        required=True,
        help='The output directory of clean reads to create.',
        action=core.CreateDir
    )
    '''
    return parser.parse_args()


def main():
    from curb.main import main
    args = get_args()
    main(args)<commit_msg>Add output dir.<commit_after>#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
(c) 2014 <NAME> || http://faircloth-lab.org/
All rights reserved.

This code is distributed under a 3-clause BSD license. Please see
LICENSE.txt for more information.

Created on 31 January 2014 11:38 PST (-0800)
"""

from __future__ import absolute_import
#import os
import argparse
from curb import core


def get_args():
    parser = argparse.ArgumentParser(
        description="Run constraint tests using RAxML",
        formatter_class=argparse.ArgumentDefaultsHelpFormatter
    )
    parser.add_argument(
        '--config',
        required=True,
        help='Path to a YAML config file with constraint info.',
        action=core.FullPaths
    )
    parser.add_argument(
        '--alignments',
        required=True,
        help='A directory of PHYLIP alignments to use for tree inference.',
        action=core.FullPaths,
        type=core.is_dir
    )
    parser.add_argument(
        '--output',
        required=True,
        help='The output directory for results.',
        action=core.CreateDir
    )
    return parser.parse_args()


def main():
    from curb.main import main
    args = get_args()
    main(args)
{'fraction_non_alphanumeric': 0.10386965376782077, 'fraction_numerical': 0.016293279022403257, 'mean_word_length': 2.6277695716395866, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '299527', 'n_tokens_mistral': 761, 'n_tokens_neox': 697, 'n_words': 212}