# HG changeset patch
# User cropgeeks
# Date 1520416922 18000
# Node ID df76e58799e723b21e6d60454fc1b3b378b31968
# Parent  3f84a298c6ca0311c79c42f3cfd723f380e4b1d0
Uploaded

diff -r 3f84a298c6ca -r df76e58799e7 FlapjackProject.py
--- a/FlapjackProject.py	Fri Mar 02 13:14:38 2018 -0500
+++ b/FlapjackProject.py	Wed Mar 07 05:02:02 2018 -0500
@@ -40,13 +40,18 @@
 
 filenames = {}
 
+favAlleleHeaders = []
+
 def splitfile(my_file, sample_data, isSample):
     temp_parents = parents
     header = ''
     fj_header = ''
     with open(my_file) as infile:
         for line in infile:
-            if line[:2] == '# ':
+            if line.lower().startswith("# fjfav"):
+                favAlleleHeaders.append(line)
+                continue
+            elif line[:2] == '# ':
                 fj_header += line
             elif header == '':
                 if fj_header == '':
@@ -111,6 +116,11 @@
                             filename = filenames.get(my_file + "_" + group+'_'+cycle)
                             f=open(filename, "a+")
                         f.write('%s' % line)
+    for key in filenames:
+        fname = filenames[key]
+        f = open(fname, "a+")
+        for fav in favAlleleHeaders:
+            f.write(fav)