diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 21 |
1 files changed, 10 insertions, 11 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 2d02e195..d248dee2 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -131,16 +131,15 @@ def check_results(ps,ts): if cmd == 'run': if options.remove_missing_phenotypes: raise Exception('Can not use --remove-missing-phenotypes with LMM2') - snp_iterator = tsvreader.geno_iter(options.geno) n = len(y) m = g.shape[1] - ps, ts = run_gwas('other',n,m,k,y,g.T) + ps, ts = run_gwas('other',n,m,k,y,g) # <--- pass in geno by SNP check_results(ps,ts) elif cmd == 'iterator': if options.remove_missing_phenotypes: raise Exception('Can not use --remove-missing-phenotypes with LMM2') - snp_iterator = tsvreader.geno_iter(options.geno) - ps, ts = gn2_load_redis_iter('testrun_iter','other',k,y,snp_iterator) + geno_iterator = tsvreader.geno_iter(options.geno) + ps, ts = gn2_load_redis_iter('testrun_iter','other',k,y,geno_iterator) check_results(ps,ts) elif cmd == 'redis_new': # The main difference between redis_new and redis is that missing @@ -150,10 +149,9 @@ elif cmd == 'redis_new': 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,new_code=True) + # gt = G.T + # G = None + ps, ts = gn2_load_redis('testrun','other',k,Y,G,new_code=True) check_results(ps,ts) elif cmd == 'redis': # Emulating the redis setup of GN2 @@ -174,9 +172,10 @@ elif cmd == 'redis': g = None gnt = None - gt = G.T - G = None - ps, ts = gn2_load_redis('testrun','other',k,Y,gt, new_code=False) + # 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': G = g |