Python get_run_info示例

示例#1

文件： bamreadcount.py 项目： agutteridge/bioinformatics_bits

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)

示例#2

文件： varscan.py 项目： agutteridge/bioinformatics_bits

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)