diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 17 |
1 files changed, 11 insertions, 6 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index e301ef1a..324c4f2c 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -57,6 +57,9 @@ parser.add_option("--maf-normalization", parser.add_option("--genotype-normalization", action="store_true", dest="genotype_normalization", default=False, help="Force genotype normalization") +parser.add_option("--remove-missing-phenotypes", + action="store_true", dest="remove_missing_phenotypes", default=False, + help="Remove missing phenotypes") parser.add_option("-q", "--quiet", action="store_false", dest="verbose", default=True, help="don't print status messages to stdout") @@ -130,11 +133,13 @@ elif cmd == 'redis': # Emulating the redis setup of GN2 G = g print "Original G",G.shape, "\n", G - if y != None: + if y != None and options.remove_missing_phenotypes: gnt = np.array(g).T Y,g,keep = phenotype.remove_missing(y,g.T,options.verbose) G = g.T print "Removed missing phenotypes",G.shape, "\n", G + else: + Y = y if options.maf_normalization: G = np.apply_along_axis( genotype.replace_missing_with_MAF, axis=0, arr=g ) print "MAF replacements: \n",G @@ -159,12 +164,12 @@ elif cmd == 'redis': 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==0.8827, "p2=%f" % p2 + assert round(sum(ps)) == 4070 + assert len(ps) == 8000 elif cmd == 'kinship': G = g print "Original G",G.shape, "\n", G - if y != None: + if y != None and options.remove_missing_phenotypes: gnt = np.array(g).T Y,g = phenotype.remove_missing(y,g.T,options.verbose) G = g.T @@ -193,11 +198,11 @@ elif cmd == 'kinship': sys.stderr.write(options.geno+"\n") k3 = round(K3[0][0],4) if options.geno == 'data/small.geno': - assert k1==0.7939, "k1=%f" % k1 + assert k1==0.8, "k1=%f" % k1 assert k2==0.7939, "k2=%f" % k2 assert k3==0.7939, "k3=%f" % k3 if options.geno == 'data/small_na.geno': - assert k1==0.7172, "k1=%f" % k1 + assert k1==0.8333, "k1=%f" % k1 assert k2==0.7172, "k2=%f" % k2 assert k3==0.7172, "k3=%f" % k3 if options.geno == 'data/test8000.geno': |