--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stderr_filter.py	Thu Dec 19 13:46:43 2019 +0000
@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+'''
+Purpose of this script is to filters some massages output
+stderr to prevent galaxy to raise the error
+'''
+import sys
+
+string_to_detect = [
+    'Karlin-Altschul parameters',
+    'slippage may introduce errors',
+    'Examining 5 or more matches is recommended',
+    'DeprecationWarning: The binary mode of fromstring is deprecated',
+]
+
+string_to_remove = [
+    ('error', 'errour'),
+    ('warning', 'alert')
+]
+input_file = sys.argv[1]
+
+with open(input_file) as f:
+    for line in f:
+        for s in string_to_detect:
+            if s in line:
+                new_line = "--" + line.lower()
+                for r in string_to_remove:
+                    new_line = new_line.replace(r[0], r[1])
+                line = new_line
+        print("parsed line:", line, file=sys.stderr)