diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/gwas.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 26 |
3 files changed, 13 insertions, 16 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/gwas.py b/wqflask/wqflask/my_pylmm/pyLMM/gwas.py index ae3769d4..247a8729 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/gwas.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/gwas.py @@ -36,7 +36,6 @@ try: from wqflask.my_pylmm.pyLMM import chunks from gn2 import uses except ImportError: - sys.stderr.write("WARNING: LMM2 standalone version missing the Genenetwork2 environment\n") has_gn2=False from standalone import uses diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 82bd7f0b..6f03eaf7 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -288,7 +288,7 @@ def run_other_old(pheno_vector, with Bench("Doing GWAS"): t_stats, p_values = GWAS(pheno_vector, - genotype_matrix, + genotype_matrix.T, kinship_matrix, restricted_max_likelihood=True, refit=False) diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index d248dee2..44d5c0f4 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -108,26 +108,25 @@ if options.geno and cmd != 'iterator': def check_results(ps,ts): print np.array(ps) print len(ps),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': info("Validating results for "+options.geno) - assert p1==0.0708, "p1=%f" % p1 - assert p2==0.1417, "p2=%f" % p2 + assert p1==0.7387, "p1=%f" % p1 + assert p2==0.7387, "p2=%f" % p2 if options.geno == 'data/small_na.geno': info("Validating results for "+options.geno) - assert p1==0.0897, "p1=%f" % p1 - assert p2==0.0405, "p2=%f" % p2 + assert p1==0.062, "p1=%f" % p1 + assert p2==0.062, "p2=%f" % p2 if options.geno == 'data/test8000.geno': info("Validating results for "+options.geno) - # assert p1==0.8984, "p1=%f" % p1 - # assert p2==0.9621, "p2=%f" % p2 assert round(sum(ps)) == 4070 assert len(ps) == 8000 info("Run completed") - + +if y is not None: + n = y.shape[0] + if cmd == 'run': if options.remove_missing_phenotypes: raise Exception('Can not use --remove-missing-phenotypes with LMM2') @@ -159,7 +158,7 @@ elif cmd == 'redis': print "Original G",G.shape, "\n", G if y is not None and options.remove_missing_phenotypes: gnt = np.array(g).T - Y,g,keep = phenotype.remove_missing(y,g.T,options.verbose) + n,Y,g,keep = phenotype.remove_missing(n,y,gnt) G = g.T print "Removed missing phenotypes",G.shape, "\n", G else: @@ -174,7 +173,6 @@ elif cmd == 'redis': # gt = G.T # G = None - mprint("G",G) ps, ts = gn2_load_redis('testrun','other',k,Y,G, new_code=False) check_results(ps,ts) elif cmd == 'kinship': @@ -182,7 +180,7 @@ elif cmd == 'kinship': print "Original G",G.shape, "\n", G if y != None and options.remove_missing_phenotypes: gnt = np.array(g).T - Y,g = phenotype.remove_missing(y,g.T,options.verbose) + n,Y,g,keep = phenotype.remove_missing(n,y,g.T) G = g.T print "Removed missing phenotypes",G.shape, "\n", G if options.maf_normalization: @@ -194,7 +192,7 @@ elif cmd == 'kinship': gnt = None if options.test_kinship: - K = kinship_full(np.copy(G),uses) + K = kinship_full(np.copy(G)) print "Genotype",G.shape, "\n", G print "first Kinship method",K.shape,"\n",K k1 = round(K[0][0],4) @@ -204,7 +202,7 @@ elif cmd == 'kinship': k2 = round(K2[0][0],4) print "Genotype",G.shape, "\n", G - K3 = kinship(G.T,uses) + K3 = kinship(G.T) print "third Kinship method",K3.shape,"\n",K3 sys.stderr.write(options.geno+"\n") k3 = round(K3[0][0],4) |