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author | Pjotr Prins | 2015-04-19 10:40:15 +0000 |
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committer | Pjotr Prins | 2015-04-19 10:40:15 +0000 |
commit | 6e4a01fbdf2ac72230346d6f474edaa56a623bfe (patch) | |
tree | 8c3bebc1e4747dd1f571a093c2fd7f76ce7054ad /wqflask/wqflask | |
parent | 3c1e043dd63fe2d65a0bd44764867254b13aba32 (diff) | |
download | genenetwork2-6e4a01fbdf2ac72230346d6f474edaa56a623bfe.tar.gz |
pylmm: can now be called from GN2 without path set
Diffstat (limited to 'wqflask/wqflask')
-rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 8 |
1 files changed, 2 insertions, 6 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 4e35a4ac..2a0c7fdc 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -19,7 +19,6 @@ from __future__ import absolute_import, print_function, division import sys import time -# import argparse import uuid import numpy as np @@ -977,6 +976,7 @@ def gn2_load_redis_iter(key,species,kinship,pheno,geno_iterator): # Note that this calling route will become OBSOLETE (we should use runlmm.py # instead) def gn2_main(): + import argparse parser = argparse.ArgumentParser(description='Run pyLMM') parser.add_argument('-k', '--key') parser.add_argument('-s', '--species') @@ -991,9 +991,5 @@ def gn2_main(): if __name__ == '__main__': print("WARNING: Calling pylmm from lmm.py will become OBSOLETE, use runlmm.py instead!") - if has_gn2: - gn2_main() - else: - fatal("Run from runlmm.py instead") - + gn2_main() |