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mecfs_bio.asset_generator.ppp_coloc_asset_generator

Asset generator for colocalizing one trait GWAS with the UKB-PPP proteins: the PPP source (protein hit table, PPP manifest fetcher, Sun et al. 2023 ST3 gene coordinates) plugged into the shared protein coloc generator, so each trait's module is a single call.

Functions:

generate_ppp_coloc_tasks 

generate_ppp_coloc_tasks(
    base_name: str,
    trait_task: Task,
    trait_model: TraitModel,
    config: ColocRunConfig = ColocRunConfig(),
    h4_threshold: float = 0.8,
    hit_table_task: ProteinHitTableTask = HAPMAP_3_PPP_HIT_TABLE_5E8,
    manifest_path: Path = EUR_DISCOVERY_PPP_MANIFEST_PATH,
) -> ColocTaskGroup

base_name: prefix of the asset ids. trait_task: the trait GWAS, genome-reference harmonized to GRCh38. trait_model: quantitative or case-control, as coloc.abf needs. manifest_path: the PPP cohort whose dense summary statistics are fetched; must match the cohort of hit_table_task.

Source code in mecfs_bio/asset_generator/ppp_coloc_asset_generator.py 
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def generate_ppp_coloc_tasks(
    base_name: str,
    trait_task: Task,
    trait_model: TraitModel,
    config: ColocRunConfig = ColocRunConfig(),
    h4_threshold: float = 0.8,
    hit_table_task: ProteinHitTableTask = HAPMAP_3_PPP_HIT_TABLE_5E8,
    manifest_path: Path = EUR_DISCOVERY_PPP_MANIFEST_PATH,
) -> ColocTaskGroup:
    """
    base_name: prefix of the asset ids.
    trait_task: the trait GWAS, genome-reference harmonized to GRCh38.
    trait_model: quantitative or case-control, as coloc.abf needs.
    manifest_path: the PPP cohort whose dense summary statistics are fetched; must match the
        cohort of hit_table_task.
    """
    source = ProteomicsColocSource(
        asset_infix="ppp",
        hit_table_task=hit_table_task,
        gene_coords_task=SUN_ET_AL_2023_ST3_EXTRACTED,
        gene_coords_reader=St3GeneCoordsReader(),
        fetcher=PppWindowFetcher(proteins=load_ppp_protein_files(manifest_path)),
    )
    return generate_protein_coloc_tasks(
        base_name=base_name,
        source=source,
        trait_task=trait_task,
        trait_model=trait_model,
        config=config,
        h4_threshold=h4_threshold,
    )