<commit_before># -----------------------------------------------------------------------------
# Copyright (c) 2014--, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# -----------------------------------------------------------------------------

from unittest import main
from os import close, remove
from shutil import copyfile, rmtree
from tempfile import mkstemp, mkdtemp
from json import dumps
from filecmp import cmp as fcmp
from os.path import exists, isdir, basename, join

from qiita_client.testing import PluginTestCase

from qp_shotgun import plugin
from qp_shotgun.humann2.humann2 import (
    make_read_sets_per_sample, make_single_fastq_gz,
    humann2, generate_humann2_analysis_commands)


class Humann2Tests(PluginTestCase):
    maxDiff = None

    def setUp(self):
        plugin("https://localhost:21174", 'register', 'ignored')
        self.params = {
            'read-set': 'fwd',
            'nucleotide-database': 'default', 'protein-database': 'default',
            'bypass-prescreen': False, 'bypass-nucleotide-index': False,
            'bypass-translated-search': False,
            'bypass-nucleotide-search': False,
            'annotation-gene-index': 8, 'evalue': 1.0,
            'metaphlan-options': '-t rel_ab', 'log-level': 'DEBUG',
            'remove-temp-output': False, 'threads': 1,
            'prescreen-threshold': 0.01, 'identity-threshold': 50.0,
            'translated-subject-coverage-threshold': 50.0,
            'translated-query-coverage-threshold': 90.0,
            'translated-alignment': 'diamond',
            'xipe': 'off', 'minpath': 'on', 'pick-frames': 'off',
            'gap-fill': 'off', 'output-format': 'biom',
            'output-max-decimals': 10, 'remove-stratified-output': False,
            'pathways': 'metacyc',
            'memory-use': 'minimum', 'remove-column-description-output': True}<commit_msg>Fixed Max Diff<commit_after># -----------------------------------------------------------------------------
# Copyright (c) 2014--, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# -----------------------------------------------------------------------------

from unittest import main
from os import close, remove
from shutil import copyfile, rmtree
from tempfile import mkstemp, mkdtemp
from json import dumps
from filecmp import cmp as fcmp
from os.path import exists, isdir, basename, join

from qiita_client.testing import PluginTestCase

from qp_shotgun import plugin
from qp_shotgun.humann2.humann2 import (
    make_read_sets_per_sample, make_single_fastq_gz,
    humann2, generate_humann2_analysis_commands)


class Humann2Tests(PluginTestCase):

    def setUp(self):
        self.maxDiff = None
        plugin("https://localhost:21174", 'register', 'ignored')
        self.params = {
            'read-set': 'fwd',
            'nucleotide-database': 'default', 'protein-database': 'default',
            'bypass-prescreen': False, 'bypass-nucleotide-index': False,
            'bypass-translated-search': False,
            'bypass-nucleotide-search': False,
            'annotation-gene-index': 8, 'evalue': 1.0,
            'metaphlan-options': '-t rel_ab', 'log-level': 'DEBUG',
            'remove-temp-output': False, 'threads': 1,
            'prescreen-threshold': 0.01, 'identity-threshold': 50.0,
            'translated-subject-coverage-threshold': 50.0,
            'translated-query-coverage-threshold': 90.0,
            'translated-alignment': 'diamond',
            'xipe': 'off', 'minpath': 'on', 'pick-frames': 'off',
            'gap-fill': 'off', 'output-format': 'biom',
            'output-max-decimals': 10, 'remove-stratified-output': False,
            'pathways': 'metacyc',
            'memory-use': 'minimum', 'remove-column-description-output': True}
{'fraction_non_alphanumeric': 0.19655344655344656, 'fraction_numerical': 0.016483516483516484, 'mean_word_length': 2.266721044045677, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4541690', 'n_tokens_mistral': 1207, 'n_tokens_neox': 1117, 'n_words': 295}