<commit_before># -*- coding: cp936 -*-
"""
Usage: python RNASeq_pipeline.py -p parameter_file.txt
-h help
-p parameter file				*[No default value]
"""


if __name__ == "__main__":
## Import modules
    import matplotlib
    matplotlib.use('Agg')
    import sys, getopt
    import rnaseq_pipeline.pipeline
    pipeline = rnaseq_pipeline.pipeline
    import rnaseq_pipeline,helper
    helper = rnaseq_pipeline.helper
    import subprocess
    
    list_args = sys.argv[1:]
    
    if '-h' in list_args:
        print __doc__
        sys.exit(0)
    elif len(list_args) <2 or '-p' not in list_args:
        print __doc__
        sys.exit(0)
    else:
        param, parameter_file, updates = helper.update_parameters(list_args)
       
    
    #if we resume we specify the old parameter file
    helper.initialize_standard(param)
    helper.write_updated_file(updates, param, parameter_file)

    helper.initialize_qsub(param)
    helper.readFastqFilenames(param)
    helper.initialize_logfiles(param)
    
    helper.writeLog('Initializing all module parameters ... \n',param)
    pipeline.initialize_all(param) 

    helper.writeLog('Initializing successful!\n',param)    
    helper.writeLog('####################################################\n',param)    
    
## run pipeline<commit_msg>fixed type in import<commit_after># -*- coding: cp936 -*-
"""
Usage: python RNASeq_pipeline.py -p parameter_file.txt
-h help
-p parameter file				*[No default value]
"""


if __name__ == "__main__":
## Import modules
    import matplotlib
    matplotlib.use('Agg')
    import sys, getopt
    import rnaseq_pipeline.pipeline
    pipeline = rnaseq_pipeline.pipeline
    import rnaseq_pipeline.helper
    helper = rnaseq_pipeline.helper
    import subprocess
    
    list_args = sys.argv[1:]
    
    if '-h' in list_args:
        print __doc__
        sys.exit(0)
    elif len(list_args) <2 or '-p' not in list_args:
        print __doc__
        sys.exit(0)
    else:
        param, parameter_file, updates = helper.update_parameters(list_args)
       
    
    #if we resume we specify the old parameter file
    helper.initialize_standard(param)
    helper.write_updated_file(updates, param, parameter_file)

    helper.initialize_qsub(param)
    helper.readFastqFilenames(param)
    helper.initialize_logfiles(param)
    
    helper.writeLog('Initializing all module parameters ... \n',param)
    pipeline.initialize_all(param) 

    helper.writeLog('Initializing successful!\n',param)    
    helper.writeLog('####################################################\n',param)    
    
## run pipeline
{'fraction_non_alphanumeric': 0.13410404624277455, 'fraction_numerical': 0.005394990366088632, 'mean_word_length': 3.1403508771929824, 'pattern_counts': {'":': 2, '<': 5, '<?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': '3312900', 'n_tokens_mistral': 810, 'n_tokens_neox': 805, 'n_words': 180}