Module molcrawl.rna.utils.config

Classes

class CellxGenePreparationConfig (output_dir: str = 'learning_source_dummy/rna',
num_worker: int = 8,
size_workload: int = 10000,
census_version: str = '2023-12-15',
min_counts_genes: int = 2,
sqrt_scale_factor: float = 0)

Expand source code

@dataclass
class CellxGenePreparationConfig:
    # Output directory where the preparation will be made
    output_dir: str = RNA_DATASET_DIR

    # Num of worker to use during parallel processing.
    num_worker: int = 8

    # Size of list of ids to give to each worker, save file will have `size_workload` number of ids in them.
    size_workload: int = 10000

    # Version of the CellxGene census
    census_version: str = "2023-12-15"

    # Filter condition to filter genes with few counts across a dataset.
    min_counts_genes: int = 2

    # Sqrt-scaling factor C for per-tissue cell subsampling.
    # Each tissue retains min(N, C * sqrt(N)) cells drawn without replacement.
    # Set to 0 (or omit) to disable subsampling and use all cells.
    sqrt_scale_factor: float = 0

CellxGenePreparationConfig(output_dir: str = 'learning_source_dummy/rna', num_worker: int = 8, size_workload: int = 10000, census_version: str = '2023-12-15', min_counts_genes: int = 2, sqrt_scale_factor: float = 0)

Instance variables

var census_version : str

var min_counts_genes : int

var num_worker : int

var output_dir : str

var size_workload : int

var sqrt_scale_factor : float

class RnaConfig (data_preparation: CellxGenePreparationConfig = <factory>)

Expand source code

@dataclass
class RnaConfig(Config):
    data_preparation: CellxGenePreparationConfig = field(default_factory=CellxGenePreparationConfig)

    def __post_init__(self):
        if not isinstance(self.data_preparation, CellxGenePreparationConfig):  # type: ignore[misc]
            self.data_preparation = CellxGenePreparationConfig(**self.data_preparation)  # type: ignore[arg-type]

RnaConfig(data_preparation: molcrawl.rna.utils.config.CellxGenePreparationConfig = )

Ancestors

• Config

Instance variables

var data_preparation : CellxGenePreparationConfig

Inherited members

• Config:
  • from_file