Python Tools Reference

Submodules

• pod5_convert_from_fast5
  • OutputHandler
    • OutputHandler.__init__()
    • OutputHandler.close_all()
    • OutputHandler.get_writer()
    • OutputHandler.resolve_one_to_one_path()
    • OutputHandler.resolve_output_path()
    • OutputHandler.set_input_complete()
  • QueueManager
    • QueueManager.__init__()
    • QueueManager.await_data()
    • QueueManager.await_request()
    • QueueManager.enqueue_data()
    • QueueManager.enqueue_exception()
    • QueueManager.enqueue_input()
    • QueueManager.enqueue_request()
    • QueueManager.get_exception()
    • QueueManager.get_input()
    • QueueManager.shutdown()
  • StatusMonitor
    • StatusMonitor.__init__()
    • StatusMonitor.close()
    • StatusMonitor.increment_reads()
    • StatusMonitor.total_files
    • StatusMonitor.total_reads
    • StatusMonitor.update_reads_total()
    • StatusMonitor.write()
  • convert_datetime_as_epoch_ms()
  • convert_fast5_end_reason()
  • convert_fast5_file()
  • convert_fast5_file_chunk()
  • convert_fast5_files()
  • convert_fast5_read()
  • convert_from_fast5()
  • convert_run_info()
  • decode_str()
  • get_read_from_fast5()
  • handle_exception()
  • is_multi_read_fast5()
  • issue_not_multi_read_exception()
  • logged()
  • logged_all()
  • main()
  • process_conversion_tasks()
  • terminate_processes()
• pod5_convert_to_fast5
  • StatusMonitor
    • StatusMonitor.__init__()
    • StatusMonitor.formatted_sample_count
    • StatusMonitor.increment()
    • StatusMonitor.print_status()
    • StatusMonitor.running
    • StatusMonitor.sample_rate
    • StatusMonitor.samples_mb
    • StatusMonitor.time_elapsed
  • convert_pod5_to_fast5()
  • convert_to_fast5()
  • main()
  • write_pod5_record_to_fast5()
• pod5_filter
  • filter_pod5()
  • main()
  • parse_ids()
• pod5_subset
  • assert_filename_template()
  • assert_overwrite_ok()
  • calculate_transfers()
  • create_default_filename_template()
  • launch_subsetting()
  • main()
  • parse_csv_mapping()
  • parse_direct_mapping_targets()
  • parse_json_mapping()
  • parse_table_mapping()
  • resolve_targets()
  • subset_pod5()
  • subset_pod5s_with_mapping()
• pod5_inspect
  • do_debug_command()
  • do_read_command()
  • do_reads_command()
  • do_summary_command()
  • dump_run_info()
  • format_shift_scale_pair()
  • format_shift_scale_pair_num()
  • inspect_pod5()
  • main()
• pod5_repack
  • main()
  • repack_pod5()
  • repack_pod5_file()
• pod5_merge
  • assert_no_duplicate_reads()
  • main()
  • merge_pod5()
• pod5_update
  • main()
  • update_pod5()
• utils
  • is_disable_pbar()
  • is_pod5_debug()
  • iterate_inputs()