diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 10 |
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 |