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authorPjotr Prins2015-04-19 10:40:15 +0000
committerPjotr Prins2015-04-19 10:40:15 +0000
commit6e4a01fbdf2ac72230346d6f474edaa56a623bfe (patch)
tree8c3bebc1e4747dd1f571a093c2fd7f76ce7054ad /wqflask
parent3c1e043dd63fe2d65a0bd44764867254b13aba32 (diff)
downloadgenenetwork2-6e4a01fbdf2ac72230346d6f474edaa56a623bfe.tar.gz
pylmm: can now be called from GN2 without path set
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py8
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()