diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 11 |
1 files changed, 8 insertions, 3 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 907a6835..738268be 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -50,6 +50,9 @@ parser.add_option("--geno",dest="geno", parser.add_option("-q", "--quiet", action="store_false", dest="verbose", default=True, help="don't print status messages to stdout") +parser.add_option("--test", + action="store_true", dest="testing", default=False, + help="Testing mode") (options, args) = parser.parse_args() @@ -76,9 +79,9 @@ def normalizeGenotype(G): # Run for every SNP list (num individuals) x = True - np.isnan(G) # Matrix of True/False m = G[x].mean() # Global mean value - print m + # print m s = np.sqrt(G[x].var()) # Global stddev - print s + # print s G[np.isnan(G)] = m # Plug-in mean values for missing if s == 0: G = G - m # Subtract the mean @@ -92,6 +95,7 @@ gn = [] for snp in g: gn.append( normalizeGenotype(snp) ) +gn = g gn = np.array(gn) print("After1",gn) gnT = gn.T @@ -99,6 +103,7 @@ print("After",gnT) # G = gnT G = gnT print "G shape",G.shape +# sys.exit(1) # assert(G[0,0]==-2.25726341) # Remove individuals with missing phenotypes @@ -111,5 +116,5 @@ if v.sum(): k = k[keep,:][:,keep] if cmd == 'redis': - ps, ts = gn2_load_redis('testrun','other',k,y,G) + ps, ts = gn2_load_redis('testrun','other',np.array(k),y,G,options.testing) print np.array(ps) |