diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 28 |
1 files changed, 16 insertions, 12 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 80478368..7a77ad0a 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -98,16 +98,20 @@ if options.geno: if cmd == 'redis': # Emulating the redis setup of GN2 - gn = [] - for ind_g in g: - gn.append( genotype.normalize(ind_g) ) - gnt = np.array(gn).T - if y: - Y,G = phenotype.remove_missing(y,gnt,options.verbose) - print "G",G.shape,G - else: - G = gnt - ps, ts = gn2_load_redis('testrun','other',k,Y,G,options.testing) + G = g + print "Original G",G.shape, "\n", G + if y != None: + gnt = np.array(g).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) + + ps, ts = gn2_load_redis('testrun','other',k,Y,G.T) print np.array(ps) print round(ps[0],4) assert(options.testing and round(ps[0],4)==0.7262) @@ -116,8 +120,8 @@ if cmd == 'redis': elif cmd == 'kinship': G = g print "Original G",G.shape, "\n", G - if y: - gnt = np.array(gn).T + if y != None: + gnt = np.array(g).T Y,g = phenotype.remove_missing(y,g.T,options.verbose) G = g.T print "Removed missing phenotypes",G.shape, "\n", G |