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mecfs_bio.asset_generator.concrete_magma_asset_generator

Generates MAGMA tasks using standard reference data

Functions:

concrete_magma_assets_generate 

concrete_magma_assets_generate(
    base_name: str,
    raw_gwas_data_task: Task,
    fmt: ValidGwaslabFormat,
    sample_size: int,
    pre_pipe: DataProcessingPipe = IdentityPipe(),
    gget_settings: GGetSettings | None = GGetSettings(50),
    number_of_bars: int = 20,
) -> MagmaTaskGeneratorFromRaw

Function to generate tasks that apply MAGMA to a GWAS summary statistics dataset using standard reference data.

Source code in mecfs_bio/asset_generator/concrete_magma_asset_generator.py 
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def concrete_magma_assets_generate(
    base_name: str,
    raw_gwas_data_task: Task,
    fmt: ValidGwaslabFormat,
    sample_size: int,
    pre_pipe: DataProcessingPipe = IdentityPipe(),
    gget_settings: GGetSettings | None = GGetSettings(50),
    number_of_bars: int = 20,
) -> MagmaTaskGeneratorFromRaw:
    """
    Function to generate tasks that apply MAGMA to a GWAS summary statistics dataset using standard reference data.
    """
    return MagmaTaskGeneratorFromRaw.create(
        raw_gwas_data_task=raw_gwas_data_task,
        base_name=base_name,
        sample_size=sample_size,
        magma_binary_task=MAGMA_1_1_BINARY_EXTRACTED,
        gene_loc_file_task=MAGMA_ENSEMBL_GENE_LOCATION_REFERENCE_DATA_BUILD_37_RAW,
        magma_ld_ref_task=MAGMA_EUR_BUILD_37_1K_GENOMES_EXTRACTED,
        tissue_expression_gene_set_task=GTEx_V10_MEDIAN_TISSUE_EXPRESSION_RNA_SEQ_PREP_FOR_MAGMA,
        fmt=fmt,
        pre_pipe=pre_pipe,
        gene_thesaurus_task=GENE_THESAURUS,
        gget_settings=gget_settings,
        number_of_bars=number_of_bars,
    )