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authorPjotr Prins2015-04-18 09:40:57 +0000
committerPjotr Prins2015-04-18 09:40:57 +0000
commit02660b9406a97943d4c33946250fc3f08b80c556 (patch)
tree2733af377fa1fc1fc071f61e7dcf5d06311a5510 /wqflask
parenta1d8f68d5428a4ceec9a2d9a771b000ecabec5e6 (diff)
downloadgenenetwork2-02660b9406a97943d4c33946250fc3f08b80c556.tar.gz
pylmm: fix integration problems
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py11
1 files changed, 6 insertions, 5 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 6fff5f1d..618f8332 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -854,22 +854,23 @@ def gwas_with_redis(key,species,new_code=True):
debug("Updating REDIS percent_complete=%d" % (round(i*100.0/total)))
progress_set_func(update_tempdata)
- def narray(key):
- print(key)
- v = params[key]
+ def narray(t):
+ info("Type is "+t)
+ v = params[t]
if v is not None:
v = np.array(v).astype(np.float)
print(v)
return v
- def narrayT(key):
- m = narray(key)
+ def narrayT(t):
+ m = narray(t)
if m is not None:
return m.T
return m
# We are transposing before we enter run_gwas - this should happen on the webserver
# side (or when reading data from file)
+ print(params)
k = narray('kinship_matrix')
g = narrayT('genotype_matrix')
y = narray('pheno_vector')