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| author | Pjotr Prins | 2015-03-15 14:25:07 +0300 |
|---|---|---|
| committer | Pjotr Prins | 2015-03-15 14:25:07 +0300 |
| commit | 31dc2a62727d14e0eab154a1e2400fd7cf587b42 (patch) | |
| tree | 3a99b60f5e5d15cb78f3422713106ff4196b3c39 | |
| parent | c48d1b4415a455a1f96ddbe8f2f89cf88b2dc283 (diff) | |
| download | genenetwork2-31dc2a62727d14e0eab154a1e2400fd7cf587b42.tar.gz | |
A little cleanup
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 4 |
2 files changed, 5 insertions, 4 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index bfb95045..5aa27106 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -333,8 +333,8 @@ def calculate_kinship_new(genotype_matrix, temp_data=None): Call the new kinship calculation where genotype_matrix contains inds (columns) by snps (rows). """ - G = np.apply_along_axis( genotype.normalize, axis=1, arr=genotype_matrix.T) - return kinship(G),G.T + G = np.apply_along_axis( genotype.normalize, axis=0, arr=genotype_matrix) + return kinship(G.T),G def calculate_kinship_old(genotype_matrix, temp_data=None): """ @@ -749,7 +749,6 @@ def gn2_redis(key,species): print('pheno', np.array(params['pheno_vector'])) geno = np.array(params['genotype_matrix']) print('geno', geno.shape, geno) - # sys.exit(1) if species == "human" : ps, ts = run_human(pheno_vector = np.array(params['pheno_vector']), diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 469ba6c9..6bb79856 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -116,7 +116,9 @@ if cmd == 'redis': g = None gnt = None - ps, ts = gn2_load_redis('testrun','other',k,Y,G.T) + gt = G.T + G = None + ps, ts = gn2_load_redis('testrun','other',k,Y,gt) print np.array(ps) # Test results p1 = round(ps[0],4) |