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authorPjotr Prins2016-02-25 12:57:53 +0000
committerPjotr Prins2016-04-20 09:48:52 +0000
commit84fef98c7929d3d42e1a7efa33bff74cbbb468c7 (patch)
tree0a8fed7c732a61a683a175ae54d3c1ec8f2577b7 /wqflask
parentf755e7d4b478e8acc9613d663e40c2a0aca7c18f (diff)
downloadgenenetwork2-84fef98c7929d3d42e1a7efa33bff74cbbb468c7.tar.gz
[PATCH 049/100] SNP_PATH: removal
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py12
1 files 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