CLAM.fdr_peak.MP.py 文件源码

def write_parameter_log(options, output_dir):
    """
    Write paramter values to a log file, named by current time.
    """
    merge_method_dict={1:'narrowPeak', 2:'broadPeak'}
    correction_method_dict={1:'Bonferroni', 2:'BH_FDR'}
    with open(output_dir+'/CLAM_Peaker.Parameters.'+ strftime("%Y%m%d_%H%M") + '.txt', 'w') as log:
        log.write('CLAM Peaker ' + __version__ + '\n')
        log.write('resume: ' + str(options.resume) + '\n')
        log.write('verbose: ' + str(options.verbose) + '\n')
        log.write('output_dir:' + str(options.output_dir) + '\n')
        log.write('tmp_dir: ' + str(options.tmp_dir) + '\n')
        log.write('peak_file: ' + str(options.peak_file) + '\n')
        log.write('is_stranded: ' + str(options.is_stranded) + '\n')
        log.write('extend: ' + str(options.extend) + '\n')
        log.write('pval_cutoff: ' + str(options.pval_cutoff) + '\n')
        log.write('merge_size: ' + str(options.merge_size) + '\n')
        log.write('max_iter: ' + str(options.max_iter) + '\n')
        log.write('gtf: ' + str(options.gtf) + '\n')
        log.write('seed: ' + str(options.seed) + '\n')
        log.write('merge_method: ' + merge_method_dict[options.merge_method] + '\n')
        log.write('correction_method: ' + correction_method_dict[options.correction_method] + '\n')
        log.write('thread: ' + str(options.nb_proc) + '\n')