From 84fef98c7929d3d42e1a7efa33bff74cbbb468c7 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 25 Feb 2016 12:57:53 +0000
Subject: [PATCH 049/100] SNP_PATH: removal

---
 wqflask/wqflask/marker_regression/marker_regression.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index e9cfb06d..1b32b05b 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -1069,7 +1069,11 @@ class MarkerRegression(object):
         return trimmed_genotype_data
     
 def create_snp_iterator_file(group):
-    plink_file_base = os.path.join(webqtlConfig.PYLMM_PATH, group)
+    """ 
+    This function is only called by main below
+    """
+    raise Exception("Paths are undefined here")
+    plink_file_base = os.path.join(webqtlConfig.TMPDIR, group)
     plink_input = input.plink(plink_file_base, type='b')
     
     data = dict(plink_input = list(plink_input),
@@ -1128,7 +1132,5 @@ def get_markers_from_csv(included_markers, p_values, group_name):
 
     return markers
     
-if __name__ == '__main__':
-    import cPickle as pickle
-    import gzip
-    create_snp_iterator_file("HLC")
+ if __name__ == '__main__':
+     import cPickle as pickle
-- 
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