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()
  • main()
  • process_conversion_tasks()
• 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_view
  • Field
    • Field.docs
    • Field.expr
  • assert_unique_acquisition_id()
  • format_view_table()
  • get_field_or_raise()
  • get_reads_tables()
  • join_reads_to_run_info()
  • join_workers()
  • launch_view_workers()
  • main()
  • parse_read_table_chunks()
  • parse_reads_table_all()
  • parse_reads_table_batch()
  • parse_run_info_table()
  • print_fields()
  • resolve_output()
  • select_fields()
  • view_pod5()
  • worker_process()
  • write()
  • write_header()
• pod5_filter
  • filter_pod5()
  • filter_reads()
  • main()
  • parse_read_id_targets()
• pod5_subset
  • WorkQueue
    • WorkQueue.__init__()
    • WorkQueue.join()
    • WorkQueue.shutdown()
  • assert_filename_template()
  • assert_overwrite_ok()
  • calculate_transfers()
  • column_keys_from_template()
  • create_default_filename_template()
  • default_filename_template()
  • fstring_to_polars()
  • get_separator()
  • launch_subsetting()
  • main()
  • overall_progress()
  • parse_csv_mapping()
  • parse_source()
  • parse_source_process()
  • parse_sources()
  • parse_table_mapping()
  • process_subset_tasks()
  • resolve_output_targets()
  • subset_pod5()
  • subset_pod5s_with_mapping()
  • subset_reads()
• pod5_merge
  • assert_no_duplicate_reads()
  • main()
  • merge_pod5()
• 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_recover
  • RecoveredData
    • RecoveredData.__init__()
    • RecoveredData.files_with_errors
    • RecoveredData.reads
    • RecoveredData.run_infos
    • RecoveredData.signal_rows
  • do_consistency_check()
  • is_file_ok()
  • main()
  • recover_pod5()
• pod5_repack
  • main()
  • repack_pod5()
  • repack_pod5_file()
  • resolve_overwrite()
• pod5_update
  • main()
  • update_pod5()
• parsers
  • SubcommandHelpFormatter
  • add_force_overwrite_argument()
  • add_recursive_argument()
  • pod5_convert_from_fast5_argparser()
  • pod5_convert_to_fast5_argparser()
  • prepare_pod5_convert()
  • prepare_pod5_filter_argparser()
  • prepare_pod5_inspect_argparser()
  • prepare_pod5_merge_argparser()
  • prepare_pod5_recover_argparser()
  • prepare_pod5_repack_argparser()
  • prepare_pod5_subset_argparser()
  • prepare_pod5_update_argparser()
  • prepare_pod5_view_argparser()
  • run_tool()
• utils
  • assert_inputs_exist()
  • assert_no_duplicate_filenames()
  • collect_inputs()
  • init_logging()
  • is_disable_pbar()
  • is_pod5_debug()
  • logged()
  • logged_all()
  • search_path()
  • search_paths()
  • terminate_processes()
  • pl_format_empty_string()
  • pl_format_read_id()
• main
  • main()