<commit_before>#!/usr/bin/env python

__author__ = "<NAME>"
__copyright__ = "Copyright 2012, The QIIME Project"
__credits__ = ["<NAME>", "<NAME>", "<NAME>"]
__license__ = "GPL"
__version__ = "1.5.0-dev"
__maintainer__ = "<NAME>"
__email__ = "<EMAIL>"
__status__ = "Development"

from os import walk
from os.path import exists, join
from qiime.workflow.util import WorkflowError
from qiime.parse import parse_taxa_summary_table
from qiime.compare_taxa_summaries import compare_taxa_summaries

assignment_method_choices = ['rdp','blast','rtax','mothur','tax2tree', 'usearch']

def format_output(compare_tables, separator):
    """Formats the output from generate_taxa_compare_table into {level: [write_ready_list]}"""
    result = {}
    for key in compare_tables.iterkeys():<commit_msg>Add uclust to list of recognized methods<commit_after>#!/usr/bin/env python

__author__ = "<NAME>"
__copyright__ = "Copyright 2012, The QIIME Project"
__credits__ = ["<NAME>", "<NAME>", "<NAME>"]
__license__ = "GPL"
__version__ = "1.5.0-dev"
__maintainer__ = "<NAME>"
__email__ = "<EMAIL>"
__status__ = "Development"

from os import walk
from os.path import exists, join
from qiime.workflow.util import WorkflowError
from qiime.parse import parse_taxa_summary_table
from qiime.compare_taxa_summaries import compare_taxa_summaries

assignment_method_choices = ['rdp','blast','rtax','mothur','tax2tree','usearch','uclust']

def format_output(compare_tables, separator):
    """Formats the output from generate_taxa_compare_table into {level: [write_ready_list]}"""
    result = {}
    for key in compare_tables.iterkeys():
{'fraction_non_alphanumeric': 0.13146417445482866, 'fraction_numerical': 0.009968847352024923, 'mean_word_length': 6.647619047619048, 'pattern_counts': {'":': 0, '<': 15, '<?xml version=': 0, '>': 15, 'https://': 0, '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': '7478624', 'n_tokens_mistral': 558, 'n_tokens_neox': 534, 'n_words': 132}