finngen_sumstat_preprocess

gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep

FinnGen sumstats preprocessing.

Source code in src/gentropy/finngen_sumstat_preprocess.py

class FinnGenSumstatPreprocessStep:
    """FinnGen sumstats preprocessing."""

    def __init__(
        self, session: Session, raw_sumstats_path: str, out_sumstats_path: str
    ) -> None:
        """Run FinnGen summary stats preprocessing step.

        Args:
            session (Session): Session object.
            raw_sumstats_path (str): Input raw summary stats path.
            out_sumstats_path (str): Output summary stats path.
        """
        # Process summary stats.
        (
            FinnGenSummaryStats.from_source(session.spark, raw_file=raw_sumstats_path)
            .df.write.mode(session.write_mode)
            .parquet(out_sumstats_path)
        )

__init__(session: Session, raw_sumstats_path: str, out_sumstats_path: str) -> None

Run FinnGen summary stats preprocessing step.

Parameters:

Name	Type	Description	Default
session	Session	Session object.	required
raw_sumstats_path	str	Input raw summary stats path.	required
out_sumstats_path	str	Output summary stats path.	required

Source code in src/gentropy/finngen_sumstat_preprocess.py

def __init__(
    self, session: Session, raw_sumstats_path: str, out_sumstats_path: str
) -> None:
    """Run FinnGen summary stats preprocessing step.

    Args:
        session (Session): Session object.
        raw_sumstats_path (str): Input raw summary stats path.
        out_sumstats_path (str): Output summary stats path.
    """
    # Process summary stats.
    (
        FinnGenSummaryStats.from_source(session.spark, raw_file=raw_sumstats_path)
        .df.write.mode(session.write_mode)
        .parquet(out_sumstats_path)
    )

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• 2023-12-21
• 2024-01-18
• Contributors