<commit_before>#
# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2013-2014. It is licensed under
# the three-clause BSD license; see doc/LICENSE.txt.
# Contact: <EMAIL>
#
import khmer
import sys
from nose import SkipTest
from nose.tools import assert_almost_equals, eq_


# DISABLING TESTS until model probabilities are finalized
"""def eq_(v1, v2):
   print >>sys.stderr, v1
   print >>sys.stderr, v2
   return True
"""


def test_alignnocov():
    ch = khmer.new_counting_hash(10, 1048576, 1)
    read = "ACCTAGGTTCGACATGTACC"
    aligner = khmer.new_readaligner(ch, 0, 0)
    for i in range(20):<commit_msg>test argument parsing of khmer.new_readaligner<commit_after>#
# This file is part of khmer, http://github.com/ged-lab/khmer/, and is
# Copyright (C) Michigan State University, 2013-2014. It is licensed under
# the three-clause BSD license; see doc/LICENSE.txt.
# Contact: <EMAIL>
#
import khmer
import sys
from nose import SkipTest
from nose.tools import assert_almost_equals, eq_


# DISABLING TESTS until model probabilities are finalized
"""def eq_(v1, v2):
   print >>sys.stderr, v1
   print >>sys.stderr, v2
   return True
"""


def test_alignnocov():
    ch = khmer.new_counting_hash(10, 1048576, 1)
    read = "ACCTAGGTTCGACATGTACC"
    try:
        aligner_bad = khmer.new_readaligner()
        assert 0, "this should fail"
    except TypeError, err:
        pass
    aligner = khmer.new_readaligner(ch, 0, 0)
    for i in range(20):
{'fraction_non_alphanumeric': 0.10481212920237311, 'fraction_numerical': 0.03493737640079104, 'mean_word_length': 3.8343949044585988, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 13, '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': '785310', 'n_tokens_mistral': 575, 'n_tokens_neox': 520, 'n_words': 165}