Update biopython/mcp_output/mcp_plugin/mcp_service.py

biopython/mcp_output/mcp_plugin/mcp_service.py

@@ -430,8 +430,13 @@ def pdb_summary(payload: dict):
 @mcp.tool(name="msa_read_fasta", description="Read a FASTA alignment file; return length and sequences")
 def msa_read_fasta(payload: dict):
     try:
+        fmt = payload.get("format", "fasta")
+        data = payload.get("data", "")
         path = payload.get("path", "")
-        alignment = AlignIO.read(path, "fasta")
+        if data:
+            alignment = AlignIO.read(StringIO(data), fmt)
+        else:
+            alignment = AlignIO.read(path, fmt)
         seqs = [{"id": rec.id, "seq": str(rec.seq)} for rec in alignment]
         aln_len = alignment.get_alignment_length() if isinstance(alignment, MultipleSeqAlignment) else None
         return {"success": True, "result": {"alignment_length": aln_len, "sequences": seqs}, "error": None}
@@ -442,8 +447,13 @@ def msa_read_fasta(payload: dict):
 @mcp.tool(name="msa_consensus", description="Compute simple consensus from FASTA alignment file")
 def msa_consensus(payload: dict):
     try:
+        fmt = payload.get("format", "fasta")
+        data = payload.get("data", "")
         path = payload.get("path", "")
-        alignment = AlignIO.read(path, "fasta")
+        if data:
+            alignment = AlignIO.read(StringIO(data), fmt)
+        else:
+            alignment = AlignIO.read(path, fmt)
         consensus = alignment.column_annotations.get("consensus") if hasattr(alignment, "column_annotations") else None
         if consensus is None:
             # naive majority rule per column