Initial commit

src/genomic_consultant/panels/aggregate.py

@@ -0,0 +1,31 @@
+from __future__ import annotations
+
+import json
+from pathlib import Path
+from typing import Dict, Iterable, List, Set
+
+
+def merge_mappings(inputs: Iterable[Path], output: Path, version: str = "merged", sources: List[str] | None = None) -> Path:
+    """
+    Merge multiple phenotype→gene mapping JSON files into one.
+    Input schema: {"phenotype_to_genes": {"HP:xxxx": ["GENE1", ...]}, "version": "...", "source": "..."}
+    """
+    merged: Dict[str, Set[str]] = {}
+    source_list: List[str] = sources or []
+    for path in inputs:
+        data = json.loads(Path(path).read_text())
+        phenos = data.get("phenotype_to_genes", {})
+        for pid, genes in phenos.items():
+            merged.setdefault(pid, set()).update(genes)
+        src_label = data.get("source") or path.name
+        source_list.append(src_label)
+
+    out = {
+        "version": version,
+        "source": ",".join(source_list),
+        "phenotype_to_genes": {pid: sorted(list(genes)) for pid, genes in merged.items()},
+        "metadata": {"merged_from": [str(p) for p in inputs]},
+    }
+    output.parent.mkdir(parents=True, exist_ok=True)
+    output.write_text(json.dumps(out, indent=2))
+    return output