Step generating a fine-mapping plan from a study index.
Source code in src/gentropy/finemapping_planner.py
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35 | class FineMappingPlanGeneratorStep:
"""Step generating a fine-mapping plan from a study index."""
def __init__(self, session: Session, input_path: str, output_path: str) -> None:
"""Resolve every registered constraint set against the study index and write the combined plan.
Args:
session (Session): Session object.
input_path (str): Path to the input study index.
output_path (str): Path to write the combined fine-mapping plan to, partitioned by route.
"""
study_index = StudyIndex.from_parquet(session, input_path)
registry = FineMappingConstraintRegistry().registry
self.plans = {
method_name: constraint_set.resolve(study_index)
for method_name, constraint_set in registry.items()
}
(
reduce(lambda p1, p2: p1 + p2, self.plans.values())
.df.coalesce(1)
.sortWithinPartitions("route", "runId", "studyId")
.write.mode(session.write_mode)
.partitionBy("route")
.parquet(output_path)
)
|