diff --git a/depedit/depedit.py b/depedit/depedit.py
index 8e69f8e..6674b00 100644
--- a/depedit/depedit.py
+++ b/depedit/depedit.py
@@ -321,6 +321,7 @@ def read_config_file(self, config_file, clear_transformations=False):
 
 		line_num = 0
 		for instruction in config_file:
+			instruction = instruction.strip()
 			line_num += 1
 			if len(instruction)>0 and not instruction.startswith(";") and not instruction.startswith("#") \
 					or instruction.startswith("#S:"):