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| author | Pjotr Prins | 2016-02-25 12:57:53 +0000 |
|---|---|---|
| committer | Pjotr Prins | 2016-04-20 09:48:52 +0000 |
| commit | 84fef98c7929d3d42e1a7efa33bff74cbbb468c7 (patch) | |
| tree | 0a8fed7c732a61a683a175ae54d3c1ec8f2577b7 | |
| parent | f755e7d4b478e8acc9613d663e40c2a0aca7c18f (diff) | |
| download | genenetwork2-84fef98c7929d3d42e1a7efa33bff74cbbb468c7.tar.gz | |
[PATCH 049/100] SNP_PATH: removal
| -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 |