diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 16 |
1 files changed, 5 insertions, 11 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index ffe25fcf..0b8830d4 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -115,18 +115,12 @@ if cmd == 'redis': assert(options.testing and round(ps[-1],4)==0.3461) elif cmd == 'kinship': G = g - print G.shape, "\n", G + print "Original G",G.shape, "\n", G if options.maf_normalization: - g1 = np.apply_along_axis( genotype.replace_missing_with_MAF, axis=0, arr=g ) - print "MAF: ",g1 - sys.exit() - for ind_g in g: - if len(gn)>=8000: break - if options.skip_genotype_normalization: - gn.append(ind_g) - else: - gn.append( genotype.normalize(ind_g) ) - G = np.array(gn) + 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) |