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

import argparse
import multiprocessing
import os
import pandas
import queue
import pandas.io.formats.excel
import re
from Bio import SeqIO

INPUT_JSON_AVG_MQ_DIR = 'input_json_avg_mq_dir'
INPUT_JSON_DIR = 'input_json_dir'
INPUT_NEWICK_DIR = 'input_newick_dir'
# Maximum columns allowed in a LibreOffice
# spreadsheet is 1024.  Excel allows for
# 16,384 columns, but we'll set the lower
# number as the maximum.  Some browsers
# (e.g., Firefox) are configured to use
# LibreOffice for Excel spreadsheets.
MAXCOLS = 1024
OUTPUT_EXCEL_DIR = 'output_excel_dir'


def annotate_table(table_df, group, annotation_dict):
    for gbk_chrome, pro in list(annotation_dict.items()):
        ref_pos = list(table_df)
        ref_series = pandas.Series(ref_pos)
        ref_df = pandas.DataFrame(ref_series.str.split(':', expand=True).values, columns=['reference', 'position'])
        all_ref = ref_df[ref_df['reference'] == gbk_chrome]
        positions = all_ref.position.to_frame()
        # Create an annotation file.
        annotation_file = "%s_annotations.csv" % group<commit_msg>Comment clarification<commit_after>#!/usr/bin/env python

import argparse
import multiprocessing
import os
import pandas
import queue
import pandas.io.formats.excel
import re
from Bio import SeqIO

INPUT_JSON_AVG_MQ_DIR = 'input_json_avg_mq_dir'
INPUT_JSON_DIR = 'input_json_dir'
INPUT_NEWICK_DIR = 'input_newick_dir'
# Maximum columns allowed in a LibreOffice
# spreadsheet is 1024.  Excel allows for
# 16,384 columns, but we'll set the lower
# number as the maximum.  Some browsers
# (e.g., Firefox on Linux) are configured
# to use LibreOffice for Excel spreadsheets.
MAXCOLS = 1024
OUTPUT_EXCEL_DIR = 'output_excel_dir'


def annotate_table(table_df, group, annotation_dict):
    for gbk_chrome, pro in list(annotation_dict.items()):
        ref_pos = list(table_df)
        ref_series = pandas.Series(ref_pos)
        ref_df = pandas.DataFrame(ref_series.str.split(':', expand=True).values, columns=['reference', 'position'])
        all_ref = ref_df[ref_df['reference'] == gbk_chrome]
        positions = all_ref.position.to_frame()
        # Create an annotation file.
        annotation_file = "%s_annotations.csv" % group
{'fraction_non_alphanumeric': 0.09362460989745876, 'fraction_numerical': 0.0115916183682568, 'mean_word_length': 4.527093596059113, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, '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': '6607589', 'n_tokens_mistral': 789, 'n_tokens_neox': 719, 'n_words': 192}