--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ecoli_serotyping/loggingFunctions.py	Fri Jan 05 15:43:14 2018 -0500
@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+"""
+    Set up the logging
+"""
+
+import logging
+import os
+
+import ectyper.definitions as D
+
+
+def initialize_logging():
+    """
+    Set up the screen and file logging.
+
+    Args:
+        None
+        
+    Returns:
+        log_file (str): The log filename
+    """
+
+    # set up DEBUG logging to file, INFO logging to STDERR
+    log_file = os.path.join(D.WORKPLACE_DIR, 'ectyper.log')
+
+    formatter = logging.Formatter(
+        '%(asctime)s %(name)-12s %(levelname)-8s %(message)s')
+
+    # logging to file
+    logging.basicConfig(
+        level=logging.DEBUG,
+        format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
+        datefmt='%m-%d %H:%M',
+        filename=log_file,
+        filemode='w')
+
+    # define a Handler which writes INFO messages or higher to the sys.stderr
+    console = logging.StreamHandler()
+    console.setFormatter(formatter)
+    console.setLevel(logging.INFO)
+
+    # add the handler to the root logger
+    logging.getLogger('').addHandler(console)
+
+    return log_file