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mecfs_bio.build_system.task.mixer.bivariate_mixer_task

Classes:

Attributes:

MIXER_BIVARIATE_FIT_JSON_PATTERN module-attribute 

MIXER_BIVARIATE_FIT_JSON_PATTERN = (
    MIXER_BIVARIATE_FIT_PREFIX_PATTERN + ".json"
)

MIXER_BIVARIATE_FIT_PREFIX_PATTERN module-attribute 

MIXER_BIVARIATE_FIT_PREFIX_PATTERN = "mixer_bivariate.fit.@"

MIXER_BIVARIATE_TEST_JSON_PATTERN module-attribute 

MIXER_BIVARIATE_TEST_JSON_PATTERN = (
    MIXER_BIVARIATE_TEST_PREFIX_PATTERN + ".json"
)

MIXER_BIVARIATE_TEST_PREFIX_PATTERN module-attribute 

MIXER_BIVARIATE_TEST_PREFIX_PATTERN = (
    "mixer_bivariate.test.@"
)

logger module-attribute 

logger = get_logger()

BivariateMixerTask

Bases: Task

Bivariate (cross-trait) MiXeR analysis.

Runs fit2 and (optionally) test2 steps, which require completed univariate fit1 results for both traits. Each BivariateMixerTask handles a single rep.

See: O.Frei et al., Bivariate causal mixture model quantifies polygenic overlap between complex traits beyond genetic correlation, Nature Communications, 2019.

Added with help from Claude

Methods:

Attributes:

apply_extract_to_test class-attribute instance-attribute 

apply_extract_to_test: bool = False

bim_file_pattern class-attribute instance-attribute 

bim_file_pattern: str = (
    "1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim"
)

chr_to_use_arg class-attribute instance-attribute 

chr_to_use_arg: str | None = None

deps property 

deps: list[Task]

extra_args class-attribute instance-attribute 

extra_args: Sequence[str] = tuple()

extract_file_pattern_gen instance-attribute 

extract_file_pattern_gen: Callable[[int], str] | None

include_test class-attribute instance-attribute 

include_test: bool = True

ld_file_pattern class-attribute instance-attribute 

ld_file_pattern: str = (
    "1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld"
)

meta property 

meta: Meta

reference_data_directory_task instance-attribute 

reference_data_directory_task: Task

rep property 

rep: int

threads class-attribute instance-attribute 

threads: int = 4

trait_1_source instance-attribute 

trait_1_source: (
    MixerDataSource | PreformattedMixerDataSource
)

trait_1_univariate_task instance-attribute 

trait_1_univariate_task: MixerTask

trait_2_source instance-attribute 

trait_2_source: (
    MixerDataSource | PreformattedMixerDataSource
)

trait_2_univariate_task instance-attribute 

trait_2_univariate_task: MixerTask

create classmethod 

create(
    asset_id: str,
    trait_1_source: MixerDataSource
    | PreformattedMixerDataSource,
    trait_2_source: MixerDataSource
    | PreformattedMixerDataSource,
    ref_data_directory_task: Task,
    trait_1_univariate_task: MixerTask,
    trait_2_univariate_task: MixerTask,
    extract_file_pattern_gen: Callable[[int], str]
    | None = default_mixer_extract_file_pattern_gen,
    extra_args: Sequence[str] = tuple(),
    chr_args: str | None = None,
    ld_file_pattern: str = "1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld",
    bim_file_pattern: str = "1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim",
    threads: int = 4,
    apply_extract_to_test: bool = False,
    include_test: bool = True,
)
Source code in mecfs_bio/build_system/task/mixer/bivariate_mixer_task.py 
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@classmethod
def create(
    cls,
    asset_id: str,
    trait_1_source: MixerDataSource | PreformattedMixerDataSource,
    trait_2_source: MixerDataSource | PreformattedMixerDataSource,
    ref_data_directory_task: Task,
    trait_1_univariate_task: MixerTask,
    trait_2_univariate_task: MixerTask,
    extract_file_pattern_gen: Callable[[int], str]
    | None = default_mixer_extract_file_pattern_gen,
    extra_args: Sequence[str] = tuple(),
    chr_args: str | None = None,
    ld_file_pattern: str = "1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld",
    bim_file_pattern: str = "1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim",
    threads: int = 4,
    apply_extract_to_test: bool = False,
    include_test: bool = True,
):
    source_meta = trait_1_source.task.meta
    meta: Meta
    if isinstance(source_meta, FilteredGWASDataMeta):
        meta = ResultDirectoryMeta(
            id=asset_id,
            trait="multi_trait",
            project="polygenic_overlap",
            sub_dir=PurePath("analysis") / "bivariate_mixer",
        )
    elif isinstance(source_meta, SimpleDirectoryMeta):
        meta = SimpleDirectoryMeta(
            id=AssetId(asset_id),
        )
    else:
        raise ValueError(f"Unknown meta {source_meta}")
    return cls(
        meta=meta,
        trait_1_source=trait_1_source,
        trait_2_source=trait_2_source,
        reference_data_directory_task=ref_data_directory_task,
        trait_1_univariate_task=trait_1_univariate_task,
        trait_2_univariate_task=trait_2_univariate_task,
        extract_file_pattern_gen=extract_file_pattern_gen,
        ld_file_pattern=ld_file_pattern,
        bim_file_pattern=bim_file_pattern,
        chr_to_use_arg=chr_args,
        extra_args=extra_args,
        threads=threads,
        apply_extract_to_test=apply_extract_to_test,
        include_test=include_test,
    )

execute 

execute(scratch_dir: Path, fetch: Fetch, wf: WF) -> Asset
Source code in mecfs_bio/build_system/task/mixer/bivariate_mixer_task.py 
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def execute(self, scratch_dir: Path, fetch: Fetch, wf: WF) -> Asset:
    chr_args = (
        ["--chr2use", self.chr_to_use_arg]
        if self.chr_to_use_arg is not None
        else []
    )
    reference_dir_asset = fetch(self.reference_data_directory_task.asset_id)
    assert isinstance(reference_dir_asset, DirectoryAsset)
    ref_mounts = {reference_dir_asset.path.resolve(): CONTAINER_REF_DIR}

    trait_1_asset = fetch(self.trait_1_univariate_task.asset_id)
    trait_2_asset = fetch(self.trait_2_univariate_task.asset_id)
    assert isinstance(trait_1_asset, DirectoryAsset)
    assert isinstance(trait_2_asset, DirectoryAsset)

    rep = self.rep
    fit_json = MIXER_FIT_JSON_PATTERN.replace("@", str(rep))
    fit_prefix = MIXER_BIVARIATE_FIT_PREFIX_PATTERN.replace("@", str(rep))
    test_prefix = MIXER_BIVARIATE_TEST_PREFIX_PATTERN.replace("@", str(rep))

    with tempfile.TemporaryDirectory(dir=os.getcwd()) as tempdir:
        tmp_path = Path(tempdir).relative_to(os.getcwd())

        # Prepare trait sumstats files in temp dir
        trait_1_stats_path = prepare_mixer_trait_input_file(
            source=self.trait_1_source,
            fetch=fetch,
            temp_dir=tmp_path,
        )
        trait_2_stats_path = prepare_mixer_trait_input_file(
            source=self.trait_2_source,
            fetch=fetch,
            temp_dir=tmp_path,
        )

        # Copy univariate fit params into temp dir
        trait1_params_name = f"trait1_params.{rep}.json"
        trait2_params_name = f"trait2_params.{rep}.json"
        shutil.copy(
            str(trait_1_asset.path / fit_json),
            str(tmp_path / trait1_params_name),
        )
        shutil.copy(
            str(trait_2_asset.path / fit_json),
            str(tmp_path / trait2_params_name),
        )

        common_args = [
            "--ld-file",
            str(CONTAINER_REF_DIR / self.ld_file_pattern),
            "--bim-file",
            str(CONTAINER_REF_DIR / self.bim_file_pattern),
            "--threads",
            str(self.threads),
        ]

        extract_args = get_mixer_extract_args(
            extract_file_pattern_gen=self.extract_file_pattern_gen,
            rep=rep,
            reference_dir_path=reference_dir_asset.path,
        )

        bivar_fit_out = str(tmp_path / fit_prefix)
        invoke_mixer(
            ["fit2"]
            + common_args
            + extract_args
            + chr_args
            + list(self.extra_args)
            + [
                "--trait1-file",
                str(trait_1_stats_path),
                "--trait2-file",
                str(trait_2_stats_path),
                "--trait1-params",
                str(tmp_path / trait1_params_name),
                "--trait2-params",
                str(tmp_path / trait2_params_name),
                "--out",
                bivar_fit_out,
            ],
            extra_mounts=ref_mounts,
        )
        bivar_fit_json = tmp_path / (fit_prefix + ".json")
        assert bivar_fit_json.exists()
        extra_test_args = []
        if self.apply_extract_to_test:
            extra_test_args.extend(extract_args)
        bivar_test_out = str(tmp_path / test_prefix)
        if self.include_test:
            invoke_mixer(
                ["test2"]
                + common_args
                + chr_args
                + extra_test_args
                + [
                    "--trait1-file",
                    str(trait_1_stats_path),
                    "--trait2-file",
                    str(trait_2_stats_path),
                    "--load-params",
                    str(bivar_fit_json),
                    "--out",
                    bivar_test_out,
                ],
                extra_mounts=ref_mounts,
            )

        # Move outputs to scratch_dir
        for suffix in (".json", ".log"):
            fit_file = Path(bivar_fit_out + suffix)
            if fit_file.exists():
                fit_file.rename(scratch_dir / fit_file.name)
            test_file = Path(bivar_test_out + suffix)
            if test_file.exists():
                test_file.rename(scratch_dir / test_file.name)

        return DirectoryAsset(scratch_dir)