diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 23 |
1 files changed, 11 insertions, 12 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 0b8830d4..80478368 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -116,28 +116,27 @@ if cmd == 'redis': elif cmd == 'kinship': G = g print "Original G",G.shape, "\n", G + if y: + gnt = np.array(gn).T + Y,g = phenotype.remove_missing(y,g.T,options.verbose) + G = g.T + print "Removed missing phenotypes",G.shape, "\n", G if options.maf_normalization: G = np.apply_along_axis( genotype.replace_missing_with_MAF, axis=0, arr=g ) print "MAF replacements: \n",G if not options.skip_genotype_normalization: G = np.apply_along_axis( genotype.normalize, axis=1, arr=G) - print G.shape, "\n", G 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),None,options) + K2 = calculate_kinship(np.copy(G.T),temp_data=None,is_testing=options.testing) + print "Genotype",G.shape, "\n", G print "GN2 Kinship method",K2.shape,"\n",K2 - K3 = kinship(G,options) + + print "Genotype",G.shape, "\n", G + K3 = kinship(np.copy(G),options) print "third Kinship method",K3.shape,"\n",K3 - sys.exit(1) - gnt = np.array(gn).T - Y,g = remove_missing_phenotypes(y,gnt,options.verbose) - G = g - print G.shape,G - K = calculate_kinship(np.copy(G),temp_data=None,is_testing=options.testing) - print G.shape,G - print "first Kinship method",K.shape,K - K = kinship(G.T,options) assert(K[0][0]==1.28) else: print "Doing nothing" |