<commit_before>#!/usr/bin/env python
import argparse
import csv
import glob
import os
import shutil
import subprocess

from datetime import datetime

from pm.log import loggers
from pm.utils.filesystem import chdir
from pm.utils import config as cf
from pm.utils import parsers

DESCRIPTION =(" Script to keep track and pre-process Illumina X Ten runs. "

"The script will work only with X Ten runs. X Ten runs generate different file "
"structure and naming than HiSeq 2000/2500. To run this script you will also need "
"bcl2fastq V >= 2.1."

"Once a run is completed and it has been pre-processed, demultiplexed data will be "
"sent to the processing server/HPC indicated in the configuration file.")

LOG = loggers.minimal_logger('Run tracker')

def check_config_options(config):
    """ Check that all needed configuration sections/config are present

    :param dict config: Parsed configuration file<commit_msg>Change mode to a+x<commit_after>#!/usr/bin/env python
import argparse
import csv
import glob
import os
import shutil
import subprocess

from datetime import datetime

from pm.log import loggers
from pm.utils.filesystem import chdir
from pm.utils import config as cf
from pm.utils import parsers

DESCRIPTION =(" Script to keep track and pre-process Illumina X Ten runs. "

"The script will work only with X Ten runs. X Ten runs generate different file "
"structure and naming than HiSeq 2000/2500. To run this script you will also need "
"bcl2fastq V >= 2.1."

"Once a run is completed and it has been pre-processed, demultiplexed data will be "
"sent to the processing server/HPC indicated in the configuration file.")

LOG = loggers.minimal_logger('Run tracker')

def check_config_options(config):
    """ Check that all needed configuration sections/config are present

    :param dict config: Parsed configuration file
{'fraction_non_alphanumeric': 0.06144643828167482, 'fraction_numerical': 0.011963023382272975, 'mean_word_length': 4.508982035928144, 'pattern_counts': {'":': 0, '<': 3, '<?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': '7449929', 'n_tokens_mistral': 530, 'n_tokens_neox': 491, 'n_words': 246}