diff options
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 12 |
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 |