PGx phenotypes: pgx phenotype|annotate (PGX-024..028, CLI-034)

CPIC lookups by allele function counts or activity values (duplications N x activity, *5/*0 = 0, total-score
fallback), Indeterminate when feasible solutions disagree or an allele is not in the guideline; per-sample
simurg.pgx/1 JSON and diplotype_annotations.tsv with PGX-026 metadata lines.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

src/simurg/cli/main.py

@@ -869,6 +869,47 @@ def pgx_star_call_cmd(
     run_guarded(rep, lambda: run_star_call(o, rep))
 
 
+def _pgx_phenotype(calls: Path, db: Path, out: Path | None, guideline: str, force: bool, log_json: bool,
+                   debug: bool, quiet: bool, name: str) -> None:  # fmt: skip
+    from simurg.pipeline.pgx_pheno import PhenoOptions, run_phenotype
+
+    if guideline not in ("cpic", "dpwg"):
+        raise typer.BadParameter("--guideline cpic|dpwg")
+    rep = _reporter(name, out or calls, log_json, debug, quiet)
+    o = PhenoOptions(calls=calls, db=db, out=out, guideline=guideline, force=force)
+    run_guarded(rep, lambda: run_phenotype(o, rep))
+
+
+@pgx_app.command("phenotype")
+def pgx_phenotype_cmd(
+    calls: Annotated[Path, typer.Option("--calls", help="Output folder of pgx star-allele call (required).")],
+    db: Annotated[Path, typer.Option("--db", help="PGx DB (required).")],
+    out: Annotated[Path | None, typer.Option("--out", help="Output folder (default: --calls).")] = None,
+    guideline: Annotated[str, typer.Option("--guideline", help="cpic|dpwg")] = "cpic",
+    force: ForceOpt = False,
+    log_json: LogJson = False,
+    debug: Debug = False,
+    quiet: Quiet = False,
+) -> None:
+    """Phenotypes from star-allele calls: per-sample PGx JSON and diplotype_annotations.tsv (CLI-034)."""
+    _pgx_phenotype(calls, db, out, guideline, force, log_json, debug, quiet, "pgx phenotype")
+
+
+@pgx_app.command("annotate", hidden=True)
+def pgx_annotate_cmd(
+    calls: Annotated[Path, typer.Option("--calls")],
+    db: Annotated[Path, typer.Option("--db")],
+    out: Annotated[Path | None, typer.Option("--out")] = None,
+    guideline: Annotated[str, typer.Option("--guideline")] = "cpic",
+    force: ForceOpt = False,
+    log_json: LogJson = False,
+    debug: Debug = False,
+    quiet: Quiet = False,
+) -> None:
+    """Alias of pgx phenotype (CLI-034)."""
+    _pgx_phenotype(calls, db, out, guideline, force, log_json, debug, quiet, "pgx annotate")
+
+
 @pgx_cn_app.command("train")
 def pgx_cn_train_cmd(
     gtcs: Annotated[Path, typer.Option("--gtcs", help="Folder searched recursively for training GTCs (required).")],