main module

mavis.main.check_completion(target_dir)

Parameters:target_dir (str) – path to the main pipeline output directory

mavis.main.check_library_dir(library_dir, verbose=False)

checks the completion of library directory and its clustering, validation and annotation subdirectories

mavis.main.check_single_job(directory)

mavis.main.convert_set_to_ranges(input_set)

mavis.main.generate_config(parser, required, optional)

Parameters:

• parser (argparse.ArgumentParser) – the main parser
• required – the argparse required arguments group
• optional – the argparse optional arguments group

mavis.main.main()

mavis.main.main_pipeline(args, configs, convert_config)

mavis.main.parse_log_details(log_file)

mavis.main.parse_runtime_from_log(log_file)

mavis.main.time_diff(start, end)

>>> time_diff('2017-04-02 15:10:48.607195', '2017-04-03 17:00:32.671809')
25.83
>>> time_diff('2017-04-03 15:10:48.607195', '2017-04-03 17:00:32.671809')
1.83

mavis.main.unique_exists(pattern, allow_none=False, get_newest=False)