# HG changeset patch
# User cropgeeks
# Date 1520421561 18000
# Node ID 819fdece454a2bbba3286e46294abc00288a8bc8
# Parent  7f0f361efcc043054a66fa0a0287bed4a4c91e37
Uploaded

diff -r 7f0f361efcc0 -r 819fdece454a FlapjackProject.py
--- a/FlapjackProject.py	Wed Mar 07 05:14:57 2018 -0500
+++ b/FlapjackProject.py	Wed Mar 07 06:19:21 2018 -0500
@@ -48,7 +48,7 @@
     fj_header = ''
     with open(my_file) as infile:
         for line in infile:
-            if line.lower().startswith("# fjfav"):
+            if line.startswith("# fjFav"):
                 favAlleleHeaders.append(line)
                 continue
             elif line[:2] == '# ':
@@ -182,10 +182,11 @@
             name = str(name)
             sfile = filenames.get(samplefile + "_" + name)
             gfile = filenames.get(genofile + "_" + name)
+            gfile += '.tmp'
             f = open(gfile, "a+")
             for fav in favAlleleHeaders:
                 f.write(fav)
-            gfile += '.tmp'
+            f.close()
             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:
                 cmd += ['-q',qtlfile]