Update app.py

app.py

@@ -24,32 +24,14 @@ logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(
 # Core Classes and Functions
 # ---------------------------
 class GenBankParser:
-    def __init__(self, fileobj):
-        self.fileobj = fileobj
+    def __init__(self, text_io):
+        self.text_io = text_io
         self.records = []
 
     def load_records(self):
-        # Ensure file is a text stream for BioPython
-        if hasattr(self.fileobj, "read") and "b" in getattr(self.fileobj, "mode", "b"):
-            # It's a BytesIO or binary stream, decode
-            text_io = io.StringIO(self.fileobj.read().decode("utf-8"))
-        elif isinstance(self.fileobj, bytes):
-            text_io = io.StringIO(self.fileobj.decode("utf-8"))
-        elif isinstance(self.fileobj, str):
-            text_io = io.StringIO(self.fileobj)
-        else:
-            # Might be a StringIO or already a text-mode file
-            try:
-                self.fileobj.seek(0)
-                _peek = self.fileobj.read(200)
-                self.fileobj.seek(0)
-                if isinstance(_peek, bytes):
-                    text_io = io.StringIO(self.fileobj.read().decode("utf-8"))
-                else:
-                    text_io = self.fileobj
-            except Exception:
-                text_io = self.fileobj
-        self.records = list(SeqIO.parse(text_io, "genbank"))
+        # Always seek to start (for re-reads)
+        self.text_io.seek(0)
+        self.records = list(SeqIO.parse(self.text_io, "genbank"))
         return self.records
 
 class AnalysisEngine:
@@ -127,12 +109,22 @@ with st.expander("ℹ️ About GeneBank Genie"):
 st.sidebar.header("Step 1. Upload GenBank File")
 gb_file = st.sidebar.file_uploader("Upload a GenBank file (.gb, .gbk)", type=["gb", "gbk"])
 if gb_file is not None:
-    # Workaround: always decode uploaded file for Biopython
+    # Always wrap the file as text for Biopython
     gb_file.seek(0)
-    gb_file_text = io.StringIO(gb_file.read().decode("utf-8"))
-    parser = GenBankParser(gb_file_text)
-    records = parser.load_records()
-    st.sidebar.success(f"Loaded {len(records)} GenBank records.")
+    gb_bytes = gb_file.read()
+    if isinstance(gb_bytes, bytes):
+        gb_text = gb_bytes.decode("utf-8")
+    else:
+        gb_text = gb_bytes
+    gb_text_io = io.StringIO(gb_text)
+    parser = GenBankParser(gb_text_io)
+    try:
+        records = parser.load_records()
+    except Exception as e:
+        st.error(f"Error parsing GenBank file: {e}")
+        records = []
+    else:
+        st.sidebar.success(f"Loaded {len(records)} GenBank records.")
 else:
     records = []
     st.warning("Upload a GenBank file to get started.")