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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/runlmm.py10
1 files changed, 5 insertions, 5 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index 44d5c0f4..52c3c80a 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -196,20 +196,20 @@ elif cmd == 'kinship':
print "Genotype",G.shape, "\n", G
print "first Kinship method",K.shape,"\n",K
k1 = round(K[0][0],4)
- K2,G = calculate_kinship_new(np.copy(G).T)
+ K2,G = calculate_kinship_new(np.copy(G))
print "Genotype",G.shape, "\n", G
print "GN2 Kinship method",K2.shape,"\n",K2
k2 = round(K2[0][0],4)
print "Genotype",G.shape, "\n", G
- K3 = kinship(G.T)
+ K3 = kinship(G)
print "third Kinship method",K3.shape,"\n",K3
sys.stderr.write(options.geno+"\n")
k3 = round(K3[0][0],4)
if options.geno == 'data/small.geno':
- assert k1==0.8, "k1=%f" % k1
- assert k2==0.7939, "k2=%f" % k2
- assert k3==0.7939, "k3=%f" % k3
+ assert k1==0.8333, "k1=%f" % k1
+ assert k2==0.9375, "k2=%f" % k2
+ assert k3==0.9375, "k3=%f" % k3
if options.geno == 'data/small_na.geno':
assert k1==0.8333, "k1=%f" % k1
assert k2==0.7172, "k2=%f" % k2