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mecfs_bio.build_system.task.mixer.mixer_bivariate_combine

Task to combine bivariate MiXeR run outputs to produce a single result.

Classes:

Attributes:

BIVARIATE_COMBINED_FIT_FILENAME_PREFIX module-attribute 

BIVARIATE_COMBINED_FIT_FILENAME_PREFIX = (
    "mixer_bivariate.fit"
)

BIVARIATE_COMBINED_TEST_FILENAME_PREFIX module-attribute 

BIVARIATE_COMBINED_TEST_FILENAME_PREFIX = (
    "mixer_bivariate.test"
)

BivariateMixerRunSource

Attributes:

rep instance-attribute 

rep: int

task instance-attribute 

task: BivariateMixerTask

MixerBivariateCombine

Bases: Task

Task to combine Bivariate MiXeR run outputs to produce a single result.

The MiXeR authors have split up the genetic variants in their reference panel into 20 random subsets. The recommended MiXeR workflow is to run MiXeR on your GWAS data using each of these 20 random subsets, then combine the results.

Use this task to combine the results of these runs

Methods:

Attributes:

deps property 

deps: list[Task]

meta property 

meta: Meta

mixer_source_runs instance-attribute 

mixer_source_runs: Sequence[BivariateMixerRunSource]

trait_1_name property 

trait_1_name: str

trait_2_name property 

trait_2_name: str

create classmethod 

create(
    asset_id: str,
    mixer_source_runs: Sequence[BivariateMixerRunSource],
)
Source code in mecfs_bio/build_system/task/mixer/mixer_bivariate_combine.py 
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@classmethod
def create(
    cls,
    asset_id: str,
    mixer_source_runs: Sequence[BivariateMixerRunSource],
):
    assert len(mixer_source_runs) >= 1
    source_meta = mixer_source_runs[0].task.meta
    meta: Meta
    if isinstance(source_meta, SimpleDirectoryMeta):
        meta = SimpleDirectoryMeta(
            id=AssetId(asset_id),
        )
    elif isinstance(source_meta, ResultDirectoryMeta):
        meta = ResultDirectoryMeta(
            id=AssetId(asset_id),
            trait=source_meta.trait,
            project=source_meta.project,
            sub_dir=source_meta.sub_dir,
        )
    else:
        raise NotImplementedError(f"Unknown source meta: {source_meta}")
    return cls(
        mixer_source_runs=mixer_source_runs,
        meta=meta,
    )

execute 

execute(scratch_dir: Path, fetch: Fetch, wf: WF) -> Asset
Source code in mecfs_bio/build_system/task/mixer/mixer_bivariate_combine.py 
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def execute(self, scratch_dir: Path, fetch: Fetch, wf: WF) -> Asset:
    with tempfile.TemporaryDirectory() as tmpdir_name:
        tmp_path = Path(tmpdir_name)
        agg_mounts = {tmp_path.resolve(): _CONTAINER_AGGREGATION_DIR}
        for source_run in self.mixer_source_runs:
            source_asset = fetch(source_run.task.asset_id)
            assert isinstance(source_asset, DirectoryAsset)
            shutil.copytree(source_asset.path, tmp_path, dirs_exist_ok=True)
            _edit_json_to_fix_trait_path(
                tmp_path
                / MIXER_BIVARIATE_FIT_JSON_PATTERN.replace(
                    "@", str(source_run.rep)
                ),
                trait_1_name=self.trait_1_name,
                trait_2_name=self.trait_2_name,
            )
            _edit_json_to_fix_trait_path(
                tmp_path
                / MIXER_BIVARIATE_TEST_JSON_PATTERN.replace(
                    "@", str(source_run.rep)
                ),
                trait_1_name=self.trait_1_name,
                trait_2_name=self.trait_2_name,
            )

        invoke_mixer_figures(
            args=[
                "combine",
                "--json",
                str(_CONTAINER_AGGREGATION_DIR / MIXER_BIVARIATE_FIT_JSON_PATTERN),
                "--out",
                str(
                    _CONTAINER_AGGREGATION_DIR
                    / BIVARIATE_COMBINED_FIT_FILENAME_PREFIX
                ),
            ],
            extra_mounts=agg_mounts,
        )

        invoke_mixer_figures(
            args=[
                "combine",
                "--json",
                str(_CONTAINER_AGGREGATION_DIR / MIXER_BIVARIATE_TEST_JSON_PATTERN),
                "--out",
                str(
                    _CONTAINER_AGGREGATION_DIR
                    / BIVARIATE_COMBINED_TEST_FILENAME_PREFIX
                ),
            ],
            extra_mounts=agg_mounts,
        )
        Path(tmp_path / (BIVARIATE_COMBINED_FIT_FILENAME_PREFIX + ".json")).rename(
            scratch_dir / (BIVARIATE_COMBINED_FIT_FILENAME_PREFIX + ".json")
        )
        Path(tmp_path / (BIVARIATE_COMBINED_TEST_FILENAME_PREFIX + ".json")).rename(
            scratch_dir / (BIVARIATE_COMBINED_TEST_FILENAME_PREFIX + ".json")
        )
        return DirectoryAsset(scratch_dir)