Update biopython/mcp_output/mcp_plugin/mcp_service.py

biopython/mcp_output/mcp_plugin/mcp_service.py

@@ -11,6 +11,25 @@ from Bio.Entrez import efetch, esearch
 
 mcp = FastMCP("biopython_service")
 
+def seqrecord_to_dict(record):
+    """Convert a SeqRecord object to a serializable dictionary."""
+    return {
+        "id": str(record.id),
+        "name": str(record.name),
+        "description": str(record.description),
+        "sequence": str(record.seq),
+        "length": len(record.seq),
+        "annotations": dict(record.annotations) if record.annotations else {},
+        "features": [
+            {
+                "type": f.type,
+                "location": str(f.location),
+                "qualifiers": dict(f.qualifiers)
+            }
+            for f in record.features
+        ] if record.features else []
+    }
+
 @mcp.tool(name="seqio_parse", description="Parse sequence data from a file.")
 def seqio_parse(file_path: str, format: str) -> dict:
     """
@@ -25,7 +44,9 @@ def seqio_parse(file_path: str, format: str) -> dict:
     """
     try:
         sequences = list(parse(file_path, format))
-        return {"success": True, "result": sequences, "error": None}
+        # Convert SeqRecord objects to serializable dictionaries
+        result = [seqrecord_to_dict(seq) for seq in sequences]
+        return {"success": True, "result": result, "error": None}
     except Exception as e:
         return {"success": False, "result": None, "error": str(e)}
 
@@ -43,7 +64,9 @@ def seqio_read(file_path: str, format: str) -> dict:
     """
     try:
         sequence = read(file_path, format)
-        return {"success": True, "result": sequence, "error": None}
+        # Convert SeqRecord object to serializable dictionary
+        result = seqrecord_to_dict(sequence)
+        return {"success": True, "result": result, "error": None}
     except Exception as e:
         return {"success": False, "result": None, "error": str(e)}