def main(shell_args): global MODE, OUTPUT_FILENAME MODE = str.upper(shell_args.mode) OUTPUT_FILENAME = shell_args.output_filename run = dir_tools.get_run_info(shell_args.run_path) init_output() for dirname in os.listdir(run['path']): # To check it is dir, not file if os.path.isdir(run['path'] + dirname): # BaseSpace (Illumina) directory structure data_path = (run['path'] + dirname + '/Data/Intensities/BaseCalls/') sample = dir_tools.get_sample_info(run['path'] + dirname) prefix = run['name'] + '_' + sample['num'] if MODE == 'READS': run_reads(data_path, sample, prefix) elif MODE == 'VARIANTS': run_variants(data_path, sample, prefix)
def main(shell_args): run = dir_tools.get_run_info(shell_args.run_path) init_output(shell_args.output_filename) execute(run, shell_args.output_filename)