oadr_cpep.cli module
Command-line interface for oadr-cpep.
A single typer app, one thin wrapper per single-function step:
- siteselect-features
fit-ridge, fit-lasso, fit-rf (single-method fits) fit-models (convenience: runs all three) apply-coefficients (this site’s solo-vs-federated outcome)
aggregator : consensus-features, aggregate-vectors
Every step takes its inputs as EXPLICIT files — no directories, no globs, nothing resolved by name — and writes its outputs to the current working directory (no output-dir option; under Nextflow that’s the process work dir, published by publishDir). The site steps read a study’s data files by panel:
Panel A : –tidy, –cpeptide Panel B : –aa, –demo, –cpeptide, –arms, –arm-subjects (arms optional)
- oadr_cpep.cli.select_features_command(site: str = typer.Option, panel: str = typer.Option, tidy: Path | None = typer.Option, aa: Path | None = typer.Option, demo: Path | None = typer.Option, cpeptide: Path | None = typer.Option, arms: Path | None = typer.Option, arm_subjects: Path | None = typer.Option, seed: int = typer.Option)
Phase 1 (site): LASSO selects features on this site’s own data (alpha chosen by CV).
- oadr_cpep.cli.fit_ridge_command(site: str = typer.Option, panel: str = typer.Option, features: Path = typer.Option, tidy: Path | None = typer.Option, aa: Path | None = typer.Option, demo: Path | None = typer.Option, cpeptide: Path | None = typer.Option, arms: Path | None = typer.Option, arm_subjects: Path | None = typer.Option, alpha: float = typer.Option, n_boot: int = typer.Option, seed: int = typer.Option)
Phase 2 (site): fit Ridge on a given feature set (vector + CV metrics + graphic).
- oadr_cpep.cli.fit_lasso_command(site: str = typer.Option, panel: str = typer.Option, features: Path = typer.Option, tidy: Path | None = typer.Option, aa: Path | None = typer.Option, demo: Path | None = typer.Option, cpeptide: Path | None = typer.Option, arms: Path | None = typer.Option, arm_subjects: Path | None = typer.Option, alpha: float = typer.Option, n_boot: int = typer.Option, seed: int = typer.Option)
Phase 2 (site): fit LASSO on a given feature set (vector + CV metrics + graphic).
- oadr_cpep.cli.fit_rf_command(site: str = typer.Option, panel: str = typer.Option, features: Path = typer.Option, tidy: Path | None = typer.Option, aa: Path | None = typer.Option, demo: Path | None = typer.Option, cpeptide: Path | None = typer.Option, arms: Path | None = typer.Option, arm_subjects: Path | None = typer.Option, n_trees: int = typer.Option, n_boot: int = typer.Option, seed: int = typer.Option)
Phase 2 (site): fit a Random Forest on a given feature set (forest + CV metrics + graphic).
- oadr_cpep.cli.fit_models_command(site: str = typer.Option, panel: str = typer.Option, features: Path = typer.Option, tidy: Path | None = typer.Option, aa: Path | None = typer.Option, demo: Path | None = typer.Option, cpeptide: Path | None = typer.Option, arms: Path | None = typer.Option, arm_subjects: Path | None = typer.Option, ridge_alpha: float = typer.Option, lasso_alpha: float = typer.Option, n_trees: int = typer.Option, n_boot: int = typer.Option, seed: int = typer.Option)
Phase 2 (site): convenience — runs fit-ridge, fit-lasso, fit-rf on the same feature set.
- oadr_cpep.cli.apply_coefficients_command(site: str = typer.Option, panel: str = typer.Option, ridge_vector: Path | None = typer.Option, lasso_vector: Path | None = typer.Option, rf_union: Path | None = typer.Option, tidy: Path | None = typer.Option, aa: Path | None = typer.Option, demo: Path | None = typer.Option, cpeptide: Path | None = typer.Option, arms: Path | None = typer.Option, arm_subjects: Path | None = typer.Option, ridge_alpha: float = typer.Option, lasso_alpha: float = typer.Option, n_boot: int = typer.Option, seed: int = typer.Option)
Phase 3 (site): this site’s own outcome using the federated results (solo vs federated).
- oadr_cpep.cli.consensus_features_command(features: List[Path] = typer.Option, min_sites: int | None = typer.Option, from_site: str | None = typer.Option)
Phase 1 (aggregator): build the consensus feature set (multi-site tally, or –from-site).
- oadr_cpep.cli.aggregate_vectors_command(vector: List[Path] = typer.Option, method: str = typer.Option)
Phase 2 (aggregator): combine the site coefficient vectors / forests (solo vs federated).