Mercurial > repos > cropgeeks > flapjack

changeset 81:819fdece454a draft

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Uploaded
author cropgeeks
date Wed, 07 Mar 2018 06:19:21 -0500
parents 7f0f361efcc0
children 348ad93dab47
files FlapjackProject.py
diffstat 1 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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]