GnomAD Linkage data ingestion

gentropy.gnomad_ingestion.LDIndexStep

LD index step.

This step is resource intensive

Suggested params: high memory machine, 5TB of boot disk, no SSDs.

Source code in src/gentropy/gnomad_ingestion.py

class LDIndexStep:
    """LD index step.

    !!! warning "This step is resource intensive"

        Suggested params: high memory machine, 5TB of boot disk, no SSDs.

    """

    def __init__(
        self,
        session: Session,
        ld_index_out: str,
        min_r2: float = LDIndexConfig().min_r2,
        ld_matrix_template: str = LDIndexConfig().ld_matrix_template,
        ld_index_raw_template: str = LDIndexConfig().ld_index_raw_template,
        ld_populations: list[LD_Population |
                             str] = LDIndexConfig().ld_populations,
        liftover_ht_path: str = LDIndexConfig().liftover_ht_path,
        grch37_to_grch38_chain_path: str = LDIndexConfig().grch37_to_grch38_chain_path,
    ) -> None:
        """Run step.

        Args:
            session (Session): Session object.
            ld_index_out (str): Output LD index path. (required)
            min_r2 (float): Minimum r2 to consider when considering variants within a window.
            ld_matrix_template (str): Input path to the gnomAD ld file with placeholder for population
            ld_index_raw_template (str): Input path to the raw gnomAD LD indices file with placeholder for population string
            ld_populations (list[LD_Population | str]): Population names derived from the ld file paths
            liftover_ht_path (str): Path to the liftover ht file
            grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates.

        Default values are provided in LDIndexConfig.
        """
        (
            GnomADLDMatrix(
                ld_matrix_template=ld_matrix_template,
                ld_index_raw_template=ld_index_raw_template,
                grch37_to_grch38_chain_path=grch37_to_grch38_chain_path,
                ld_populations=ld_populations,
                liftover_ht_path=liftover_ht_path,
            )
            .as_ld_index(min_r2)
            .df.write.partitionBy("chromosome")
            .mode(session.write_mode)
            .parquet(ld_index_out)
        )
        session.logger.info(ld_index_out)

__init__(session: Session, ld_index_out: str, min_r2: float = LDIndexConfig().min_r2, ld_matrix_template: str = LDIndexConfig().ld_matrix_template, ld_index_raw_template: str = LDIndexConfig().ld_index_raw_template, ld_populations: list[LD_Population | str] = LDIndexConfig().ld_populations, liftover_ht_path: str = LDIndexConfig().liftover_ht_path, grch37_to_grch38_chain_path: str = LDIndexConfig().grch37_to_grch38_chain_path) -> None

Run step.

Parameters:

Name	Type	Description	Default
session	Session	Session object.	required
ld_index_out	str	Output LD index path. (required)	required
min_r2	float	Minimum r2 to consider when considering variants within a window.	min_r2
ld_matrix_template	str	Input path to the gnomAD ld file with placeholder for population	ld_matrix_template
ld_index_raw_template	str	Input path to the raw gnomAD LD indices file with placeholder for population string	ld_index_raw_template
ld_populations	list[LD_Population | str]	Population names derived from the ld file paths	ld_populations
liftover_ht_path	str	Path to the liftover ht file	liftover_ht_path
grch37_to_grch38_chain_path	str	Path to the chain file used to lift over the coordinates.	grch37_to_grch38_chain_path

Default values are provided in LDIndexConfig.

Source code in src/gentropy/gnomad_ingestion.py

def __init__(
    self,
    session: Session,
    ld_index_out: str,
    min_r2: float = LDIndexConfig().min_r2,
    ld_matrix_template: str = LDIndexConfig().ld_matrix_template,
    ld_index_raw_template: str = LDIndexConfig().ld_index_raw_template,
    ld_populations: list[LD_Population |
                         str] = LDIndexConfig().ld_populations,
    liftover_ht_path: str = LDIndexConfig().liftover_ht_path,
    grch37_to_grch38_chain_path: str = LDIndexConfig().grch37_to_grch38_chain_path,
) -> None:
    """Run step.

    Args:
        session (Session): Session object.
        ld_index_out (str): Output LD index path. (required)
        min_r2 (float): Minimum r2 to consider when considering variants within a window.
        ld_matrix_template (str): Input path to the gnomAD ld file with placeholder for population
        ld_index_raw_template (str): Input path to the raw gnomAD LD indices file with placeholder for population string
        ld_populations (list[LD_Population | str]): Population names derived from the ld file paths
        liftover_ht_path (str): Path to the liftover ht file
        grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates.

    Default values are provided in LDIndexConfig.
    """
    (
        GnomADLDMatrix(
            ld_matrix_template=ld_matrix_template,
            ld_index_raw_template=ld_index_raw_template,
            grch37_to_grch38_chain_path=grch37_to_grch38_chain_path,
            ld_populations=ld_populations,
            liftover_ht_path=liftover_ht_path,
        )
        .as_ld_index(min_r2)
        .df.write.partitionBy("chromosome")
        .mode(session.write_mode)
        .parquet(ld_index_out)
    )
    session.logger.info(ld_index_out)

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• 2023-03-10
• 2024-06-30
• Contributors