diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 35 |
1 files changed, 19 insertions, 16 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 1af5a443..708c9185 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -54,9 +54,9 @@ parser.add_option("--geno",dest="geno", parser.add_option("--maf-normalization", action="store_true", dest="maf_normalization", default=False, help="Apply MAF genotype normalization") -parser.add_option("--skip-genotype-normalization", - action="store_true", dest="skip_genotype_normalization", default=False, - help="Skip genotype normalization") +parser.add_option("--genotype-normalization", + action="store_true", dest="genotype_normalization", default=False, + help="Force genotype normalization") parser.add_option("-q", "--quiet", action="store_false", dest="verbose", default=True, help="don't print status messages to stdout") @@ -100,7 +100,8 @@ if options.geno: print g.shape if cmd == 'redis_new': - # Emulating the redis setup of GN2 + # The main difference between redis_new and redis is that missing + # phenotypes are handled by the first Y = y G = g print "Original G",G.shape, "\n", G @@ -109,7 +110,7 @@ if cmd == 'redis_new': G = None ps, ts = gn2_load_redis('testrun','other',k,Y,gt,new_code=True) print np.array(ps) - print sum(ps) + print len(ps),sum(ps) # Test results p1 = round(ps[0],4) p2 = round(ps[-1],4) @@ -118,12 +119,14 @@ if cmd == 'redis_new': 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 + assert p1==0.0897, "p1=%f" % p1 + assert p2==0.0405, "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': + assert p2==0.9620, "p2=%f" % p2 + assert sum(ps) == 4070.02346579 + assert len(ps) == 8000 +elif cmd == 'redis': # Emulating the redis setup of GN2 G = g print "Original G",G.shape, "\n", G @@ -135,7 +138,7 @@ if cmd == 'redis': 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: + if options.genotype_normalization: G = np.apply_along_axis( genotype.normalize, axis=1, arr=G) g = None gnt = None @@ -144,8 +147,8 @@ if cmd == 'redis': G = None ps, ts = gn2_load_redis('testrun','other',k,Y,gt, new_code=False) print np.array(ps) - print sum(ps) - # Test results + print len(ps),sum(ps) + # Test results 4070.02346579 p1 = round(ps[0],4) p2 = round(ps[-1],4) sys.stderr.write(options.geno+"\n") @@ -153,11 +156,11 @@ if cmd == 'redis': 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 + assert p1==0.0897, "p1=%f" % p1 + assert p2==0.0405, "p2=%f" % p2 if options.geno == 'data/test8000.geno': assert p1==0.8984, "p1=%f" % p1 - assert p2==0.9623, "p2=%f" % p2 + assert p2==0.8827, "p2=%f" % p2 elif cmd == 'kinship': G = g print "Original G",G.shape, "\n", G @@ -169,7 +172,7 @@ elif cmd == 'kinship': 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: + if options.genotype_normalization: G = np.apply_along_axis( genotype.normalize, axis=1, arr=G) g = None gnt = None |