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
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64 | 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)
|