from utils import parse_command_args, process_configuration recipe_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) sys.path.append(os.path.join(recipe_path, "scripts")) from cell_quality_utils import CellQuality from io_utils import check_if_write args = parse_command_args() plate_id = args.plate_id options_config_file = args.options_config_file experiment_config_file = args.experiment_config_file config = process_configuration( plate_id, options_config=options_config_file, experiment_config=experiment_config_file, ) # Set constants control_barcodes = config["experiment"]["control_barcode_ids"] id_cols = config["options"]["core"]["cell_id_cols"] spot_parent_cols = config["options"]["core"]["cell_match_cols"]["spots"] ignore_files = config["options"]["core"]["ignore_files"] cell_filter = config["options"]["core"]["cell_quality"]["cell_filter"] quality_func = config["options"]["core"]["cell_quality"][ "categorize_cell_quality"] quality_col = config["options"]["core"]["cell_quality"]["cell_quality_column"] quality_idx = config["options"]["core"]["cell_quality"]["cell_quality_index"]
sys.excepthook = handle_excepthook # Configure experiment args = parse_command_args() logging.info(f"Args used:{args}") batch_id = args.batch_id options_config_file = args.options_config_file experiment_config_file = args.experiment_config_file split_step = args.split_step config, incomplete_sites, errored_sites = process_configuration( batch_id, step="preprocess--process-cells", options_config=options_config_file, experiment_config=experiment_config_file, ) logging.info(f"Config used:{config}") logging.info(f"Skipped incomplete sites during config processing: {incomplete_sites}") logging.info(f"Skipped errored sites during config processing: {errored_sites}") # Define variables set in the config file split_info = config["experiment"]["split"][split_step] ignore_files = config["options"]["core"]["ignore_files"] id_cols = config["options"]["core"]["cell_id_cols"] compartments = config["options"]["core"]["compartments"] parent_cols = config["options"]["core"]["cell_match_cols"] quality_func = config["options"]["core"]["cell_quality"]["categorize_cell_quality"] quality_col = config["options"]["core"]["cell_quality"]["cell_quality_column"]
sys.excepthook = handle_excepthook # Configure experiment args = parse_command_args() logging.info(f"Args used:{args}") batch_id = args.batch_id options_config_file = args.options_config_file experiment_config_file = args.experiment_config_file split_step = args.split_step config, incomplete_sites, errored_sites = process_configuration( batch_id, step="profile--normalize", options_config=options_config_file, experiment_config=experiment_config_file, ) logging.info(f"Config used:{config}") logging.info( f"Skipped incomplete sites during config processing: {incomplete_sites}") logging.info( f"Skipped errored sites during config processing: {errored_sites}") # Extract config arguments split_info = config["experiment"]["split"][split_step] perform = config["options"]["profile"]["normalize"]["perform"] # check if this step should be performed if not perform: sys.exit(
sys.excepthook = handle_excepthook # Configure experiment args = parse_command_args() logging.info(f"Args used:{args}") batch_id = args.batch_id options_config_file = args.options_config_file experiment_config_file = args.experiment_config_file split_step = args.split_step config, incomplete_sites, errored_sites = process_configuration( batch_id, step="profile--feature_select", options_config=options_config_file, experiment_config=experiment_config_file, ) logging.info(f"Config used:{config}") logging.info(f"Skipped incomplete sites during config processing: {incomplete_sites}") logging.info(f"Skipped errored sites during config processing: {errored_sites}") # Extract config arguments split_info = config["experiment"]["split"][split_step] perform = config["options"]["profile"]["feature_select"]["perform"] # check if this step should be performed if not perform: sys.exit("Config file set to perform=False, not performing {}".format(__file__)) ignore_files = config["options"]["core"]["ignore_files"]
sys.excepthook = handle_excepthook # Configure experiment args = parse_command_args() logging.info(f"Args used:{args}") batch_id = args.batch_id options_config_file = args.options_config_file experiment_config_file = args.experiment_config_file split_step = args.split_step config, incomplete_sites, errored_sites = process_configuration( batch_id, step="preprocess--summarize-plate", options_config=options_config_file, experiment_config=experiment_config_file, ) logging.info(f"Config used:{config}") logging.info(f"Skipped incomplete sites during config processing: {incomplete_sites}") logging.info(f"Skipped errored sites during config processing: {errored_sites}") # Defines the sections of the config file # Defines the variables set in the config file barcoding_cycles = config["experiment"]["barcoding_cycles"] sites_per_image_grid_side = config["experiment"]["sites_per_image_grid_side"] split_info = config["experiment"]["split"][split_step] ignore_files = config["options"]["core"]["ignore_files"] cell_filter = config["options"]["core"]["cell_quality"]["cell_filter"]