variant_index

gentropy.variant_index.VariantIndexStep

Run variant index step to only variants in study-locus sets.

Using a VariantAnnotation dataset as a reference, this step creates and writes a dataset of the type VariantIndex that includes only variants that have disease-association data with a reduced set of annotations.

Source code in src/gentropy/variant_index.py

class VariantIndexStep:
    """Run variant index step to only variants in study-locus sets.

    Using a `VariantAnnotation` dataset as a reference, this step creates and writes a dataset of the type `VariantIndex` that includes only variants that have disease-association data with a reduced set of annotations.
    """

    def __init__(
        self: VariantIndexStep,
        session: Session,
        variant_annotation_path: str,
        credible_set_path: str,
        variant_index_path: str,
    ) -> None:
        """Run VariantIndex step.

        Args:
            session (Session): Session object.
            variant_annotation_path (str): Variant annotation dataset path.
            credible_set_path (str): Credible set dataset path.
            variant_index_path (str): Variant index dataset path.
        """
        # Extract
        va = VariantAnnotation.from_parquet(session, variant_annotation_path)
        credible_set = StudyLocus.from_parquet(
            session, credible_set_path, recursiveFileLookup=True
        )

        # Transform
        vi = VariantIndex.from_variant_annotation(va, credible_set)

        (
            vi.df.write.partitionBy("chromosome")
            .mode(session.write_mode)
            .parquet(variant_index_path)
        )

__init__(session: Session, variant_annotation_path: str, credible_set_path: str, variant_index_path: str) -> None

Run VariantIndex step.

Parameters:

Name	Type	Description	Default
session	Session	Session object.	required
variant_annotation_path	str	Variant annotation dataset path.	required
credible_set_path	str	Credible set dataset path.	required
variant_index_path	str	Variant index dataset path.	required

Source code in src/gentropy/variant_index.py

def __init__(
    self: VariantIndexStep,
    session: Session,
    variant_annotation_path: str,
    credible_set_path: str,
    variant_index_path: str,
) -> None:
    """Run VariantIndex step.

    Args:
        session (Session): Session object.
        variant_annotation_path (str): Variant annotation dataset path.
        credible_set_path (str): Credible set dataset path.
        variant_index_path (str): Variant index dataset path.
    """
    # Extract
    va = VariantAnnotation.from_parquet(session, variant_annotation_path)
    credible_set = StudyLocus.from_parquet(
        session, credible_set_path, recursiveFileLookup=True
    )

    # Transform
    vi = VariantIndex.from_variant_annotation(va, credible_set)

    (
        vi.df.write.partitionBy("chromosome")
        .mode(session.write_mode)
        .parquet(variant_index_path)
    )

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• 2023-01-15
• 2024-01-18
• Contributors