FinnGen study index generation step.
Source code in src/gentropy/finngen_studies.py
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53 | class FinnGenStudiesStep:
"""FinnGen study index generation step."""
def __init__(
self,
session: Session,
finngen_study_index_out: str,
finngen_phenotype_table_url: str = FinngenStudiesConfig().finngen_phenotype_table_url,
finngen_release_prefix: str = FinngenStudiesConfig().finngen_release_prefix,
finngen_summary_stats_url_prefix: str = FinngenStudiesConfig().finngen_summary_stats_url_prefix,
finngen_summary_stats_url_suffix: str = FinngenStudiesConfig().finngen_summary_stats_url_suffix,
efo_curation_mapping_url: str = FinngenStudiesConfig().efo_curation_mapping_url,
sample_size: int = FinngenStudiesConfig().sample_size,
) -> None:
"""Run FinnGen study index generation step.
Args:
session (Session): Session object.
finngen_study_index_out (str): Output FinnGen study index path.
finngen_phenotype_table_url (str): URL to the FinnGen phenotype table.
finngen_release_prefix (str): FinnGen release prefix.
finngen_summary_stats_url_prefix (str): FinnGen summary stats URL prefix.
finngen_summary_stats_url_suffix (str): FinnGen summary stats URL suffix.
efo_curation_mapping_url (str): URL to the EFO curation mapping file
sample_size (int): Number of individuals that participated in sample collection, derived from finngen release metadata.
"""
_match = FinnGenStudyIndex.validate_release_prefix(finngen_release_prefix)
release_prefix = _match["prefix"]
release = _match["release"]
efo_mapping = EFOMapping.from_path(session, efo_curation_mapping_url)
study_index = FinnGenStudyIndex.from_source(
session.spark,
finngen_phenotype_table_url,
release_prefix,
finngen_summary_stats_url_prefix,
finngen_summary_stats_url_suffix,
sample_size,
)
study_index_with_efo = efo_mapping.annotate_study_index(study_index, release)
study_index_with_efo.df.coalesce(session.output_partitions).write.mode(
session.write_mode
).parquet(finngen_study_index_out)
|