Transform a ProteinQuantitativeTraitLocusStudyIndex into a standard StudyIndex.
This step resolves gene-level and protein-level annotations from the
TargetIndex (e.g. Ensembl gene IDs) and
writes a study index compatible with the downstream Open Targets genetics pipeline.
Source code in src/gentropy/pqtl_study.py
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42 | class pQTLStudyIndexTransformationStep:
"""Transform a `ProteinQuantitativeTraitLocusStudyIndex` into a standard `StudyIndex`.
This step resolves gene-level and protein-level annotations from the
`TargetIndex` (e.g. Ensembl gene IDs) and
writes a study index compatible with the downstream Open Targets genetics pipeline.
"""
def __init__(
self,
session: Session,
protein_study_index_path: str,
study_index_path: str,
target_index_path: str,
) -> None:
"""Initialise and execute the pQTL study-index transformation step.
Args:
session (Session): Active Gentropy Spark session.
protein_study_index_path (str): Path to the
`ProteinQuantitativeTraitLocusStudyIndex`.
study_index_path (str): Destination path for the resolved
`StudyIndex` Parquet dataset.
target_index_path (str): Path to the
`TargetIndex` Parquet dataset used
to map gene symbols to Ensembl gene IDs.
"""
pqtl = ProteinQuantitativeTraitLocusStudyIndex.from_parquet(
session, protein_study_index_path
)
ti = TargetIndex.from_parquet(session, target_index_path)
s = pqtl.to_study(ti)
s.df.coalesce(1).write.mode(session.write_mode).parquet(study_index_path)
|