Update biopython/mcp_output/mcp_plugin/mcp_service.py

biopython/mcp_output/mcp_plugin/mcp_service.py

@@ -48,11 +48,31 @@ def lazy_import_script(module_path, attr_name):
 
 # Biopython top-level imports (这些是安全的)
 from Bio import __version__ as bio_version
-from Bio import Entrez, SeqIO, pairwise2, Phylo, AlignIO
+from Bio import Entrez, SeqIO, Phylo, AlignIO
 from Bio.PDB import PDBParser
-from Bio.Align import MultipleSeqAlignment
+from Bio.Align import MultipleSeqAlignment, PairwiseAligner
 from Bio.Seq import Seq
-from Bio.SeqUtils import GC
+
+# GC function location varies by Biopython version
+try:
+    from Bio.SeqUtils import GC
+except ImportError:
+    try:
+        from Bio.SeqUtils import gc_fraction as GC
+    except ImportError:
+        # Fallback implementation
+        def GC(seq):
+            """Calculate GC content percentage"""
+            seq = str(seq).upper()
+            gc = seq.count('G') + seq.count('C')
+            return (gc / len(seq)) * 100 if len(seq) > 0 else 0
+
+# pairwise2 is deprecated, but keep for compatibility
+try:
+    from Bio import pairwise2
+    HAS_PAIRWISE2 = True
+except (ImportError, AttributeError):
+    HAS_PAIRWISE2 = False
 
 mcp = FastMCP("biopython")
 
@@ -335,17 +355,38 @@ def pairwise_align_globalxx(payload: dict):
         seq1 = payload.get("seq1", "")
         seq2 = payload.get("seq2", "")
         limit = int(payload.get("limit", 3))
-        aligns = pairwise2.align.globalxx(seq1, seq2)[:limit]
-        result = [
-            {
-                "seqA": a.seqA,
-                "seqB": a.seqB,
-                "score": a.score,
-                "start": a.start,
-                "end": a.end,
-            }
-            for a in aligns
-        ]
+        
+        if HAS_PAIRWISE2:
+            # Use deprecated pairwise2 if available
+            aligns = pairwise2.align.globalxx(seq1, seq2)[:limit]
+            result = [
+                {
+                    "seqA": a.seqA,
+                    "seqB": a.seqB,
+                    "score": a.score,
+                    "start": a.start,
+                    "end": a.end,
+                }
+                for a in aligns
+            ]
+        else:
+            # Use modern PairwiseAligner
+            aligner = PairwiseAligner()
+            aligner.mode = 'global'
+            aligner.match_score = 1
+            aligner.mismatch_score = 0
+            alignments = list(aligner.align(seq1, seq2))[:limit]
+            result = [
+                {
+                    "seqA": str(alignment).split('\n')[0],
+                    "seqB": str(alignment).split('\n')[2] if len(str(alignment).split('\n')) > 2 else "",
+                    "score": alignment.score,
+                    "start": 0,
+                    "end": len(seq1),
+                }
+                for alignment in alignments
+            ]
+        
         return {"success": True, "result": result, "error": None}
     except Exception as e:
         return {"success": False, "result": None, "error": str(e)}