diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 26 |
1 files changed, 25 insertions, 1 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index f17f1bd1..4268f3be 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -99,13 +99,37 @@ if options.geno: g = tsvreader.geno(options.geno) print g.shape +if cmd == 'redis_new': + # Emulating the redis setup of GN2 + Y = y + G = g + print "Original G",G.shape, "\n", G + + gt = G.T + G = None + ps, ts = gn2_load_redis('testrun','other',k,Y,gt) + print np.array(ps) + print sum(ps) + # Test results + p1 = round(ps[0],4) + p2 = round(ps[-1],4) + sys.stderr.write(options.geno+"\n") + if options.geno == 'data/small.geno': + assert p1==0.0708, "p1=%f" % p1 + assert p2==0.1417, "p2=%f" % p2 + if options.geno == 'data/small_na.geno': + assert p1==0.0958, "p1=%f" % p1 + assert p2==0.0435, "p2=%f" % p2 + if options.geno == 'data/test8000.geno': + assert p1==0.8984, "p1=%f" % p1 + assert p2==0.9623, "p2=%f" % p2 if cmd == 'redis': # Emulating the redis setup of GN2 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) + Y,g,keep = phenotype.remove_missing(y,g.T,options.verbose) G = g.T print "Removed missing phenotypes",G.shape, "\n", G if options.maf_normalization: |