--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/patch_stringmlst.sh	Fri May 15 11:44:48 2026 +0000
@@ -0,0 +1,45 @@
+#!/usr/bin/env bash
+
+# patch stringMLST.py log path: replace dbPrefix reference with cwd.
+# patches all occurrences (at line 1464 and predict section at line 1478).
+
+set -euo pipefail
+
+STRINGMLST="$PREFIX/bin/stringMLST.py"
+
+if [ ! -f "$STRINGMLST" ]; then
+    echo "SKIP: $STRINGMLST not found"
+    exit 0
+fi
+
+python3 << 'PATCH_WITH_PY'
+import os
+
+p = os.path.join(os.environ["PREFIX"], "bin", "stringMLST.py")
+with open(p) as f:
+    lines = f.readlines()
+
+original = "            log = dbPrefix+'.log'\n"
+commented = "            # log = dbPrefix+'.log'\n"
+replacement = '            log = os.path.join(os.getcwd(), "kmer.log")\n'
+
+# Count occurrences BEFORE modifying
+occurrences = lines.count(original)
+
+if occurrences == 0:
+    print("SKIP: stringMLST.py has 0 occurrences, expected at least 1")
+    exit(0)
+
+out = []
+for line in lines:
+    if line.rstrip("\n") == original.rstrip("\n"):
+        out.append(commented)
+        out.append(replacement)
+    else:
+        out.append(line)
+
+with open(p, "w") as f:
+    f.writelines(out)
+
+print("PATCHED: stringMLST.py log path fixed (%d occurrences)" % occurrences)
+PATCH_WITH_PY
\ No newline at end of file