Update app.py

app.py

@@ -60,12 +60,27 @@ def run_prediction(unknown_files, kmer_zip, seqtype, mode, identity, coverage, f
 
     # Copy unknown FASTAs
     for idx, f in enumerate(unknown_files, start=1):
-        src = getattr(f, "path", None) or getattr(f, "name", None) or str(f)
-        orig = getattr(f, "orig_name", None) or getattr(f, "filename", None) or os.path.basename(src)
+    src = getattr(f, "path", None) or getattr(f, "name", None) or str(f)
+    orig = (
+        getattr(f, "orig_name", None)
+        or getattr(f, "filename", None)
+        or os.path.basename(src)
+    )
+
+    lower = orig.lower()
+
+    # ZIP → extract FASTA files
+    if lower.endswith(".zip") or src.lower().endswith(".zip"):
+        _safe_extract_zip(src, unknown_dir)
+        continue
+
+    # FASTA file
+    if not lower.endswith((".fa", ".fasta", ".fas", ".fna")):
+        continue
+
+    dst = os.path.join(unknown_dir, os.path.basename(orig))
+    shutil.copy(src, dst)
 
-        # Ensure a valid fasta extension for readability (parser doesn't require it, but it's cleaner)
-        if not orig.lower().endswith(FASTA_EXTS):
-            orig = f"unknown_{idx}.fasta"
 
         shutil.copy(src, os.path.join(unknown_dir, os.path.basename(orig)))