# HG changeset patch
# User cropgeeks
# Date 1520417697 18000
# Node ID 7f0f361efcc043054a66fa0a0287bed4a4c91e37
# Parent  df76e58799e723b21e6d60454fc1b3b378b31968
Uploaded

diff -r df76e58799e7 -r 7f0f361efcc0 FlapjackProject.py
--- a/FlapjackProject.py	Wed Mar 07 05:02:02 2018 -0500
+++ b/FlapjackProject.py	Wed Mar 07 05:14:57 2018 -0500
@@ -116,11 +116,6 @@
                             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)
                     
                     
                     
@@ -187,6 +182,9 @@
             name = str(name)
             sfile = filenames.get(samplefile + "_" + name)
             gfile = filenames.get(genofile + "_" + name)
+            f = open(gfile, "a+")
+            for fav in favAlleleHeaders:
+                f.write(fav)
             gfile += '.tmp'
             cmd = ['java', '-cp',jarfile,'jhi.flapjack.io.cmd.CreateProject','-A','-g',gfile,'-t',sfile,'-p',project,'-n',name,'-S',separator,'-M',missing,'-C']
             if qtlfile: