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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/runlmm.py15
1 files changed, 13 insertions, 2 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index 8c0b73eb..21d9240b 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -143,13 +143,24 @@ elif cmd == 'kinship':
K = kinship_full(G,options)
print "Genotype",G.shape, "\n", G
print "first Kinship method",K.shape,"\n",K
- K2 = calculate_kinship(np.copy(G.T),temp_data=None,is_testing=options.testing)
+ K2 = calculate_kinship(np.copy(G.T),temp_data=None)
print "Genotype",G.shape, "\n", G
print "GN2 Kinship method",K2.shape,"\n",K2
print "Genotype",G.shape, "\n", G
K3 = kinship(np.copy(G),options)
print "third Kinship method",K3.shape,"\n",K3
- assert(K[0][0]==1.28)
+ sys.stderr.write(options.geno+"\n")
+ k1 = round(K[0][0],4)
+ k2 = round(K2[0][0],4)
+ k3 = round(K3[0][0],4)
+ if options.geno == 'data/small.geno':
+ assert k1==0.7939, "k1=%f" % k1
+ assert k2==0.7939, "k1=%f" % k1
+ assert k3==0.7939, "k1=%f" % k1
+ if options.geno == 'data/small_na.geno':
+ assert k1==0.7172, "k1=%f" % k1
+ assert k2==0.7172, "k1=%f" % k1
+ assert k3==0.7172, "k1=%f" % k1
else:
print "Doing nothing"