Python process_configuration示例

示例#1

文件： 1.process-spots.py 项目： gwaygenomics/pooled-cell-painting-profiling-recipe

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"]

示例#2

文件： 2.process-cells.py 项目： broadinstitute/pooled-cell-painting-profiling-recipe

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"]

示例#3

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(

示例#4

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"]

示例#5

文件： 4.image-and-segmentation-qc.py 项目： broadinstitute/pooled-cell-painting-profiling-recipe

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"]