diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 13 |
1 files changed, 8 insertions, 5 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 26485136..547ac7f1 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -140,7 +140,7 @@ elif cmd == 'kinship': if not options.skip_genotype_normalization: G = np.apply_along_axis( genotype.normalize, axis=1, arr=G) - if True: + if False: K = kinship_full(G) print "Genotype",G.shape, "\n", G print "first Kinship method",K.shape,"\n",K @@ -157,11 +157,14 @@ elif cmd == 'kinship': 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 + assert k2==0.7939, "k2=%f" % k2 + assert k3==0.7939, "k3=%f" % k3 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 + assert k2==0.7172, "k2=%f" % k2 + assert k3==0.7172, "k3=%f" % k3 + if options.geno == 'data/test8000.geno': + assert k3==1.4352, "k3=%f" % k3 + else: print "Doing nothing" |