diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 37 |
1 files changed, 27 insertions, 10 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 618f8332..5b06c9ae 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -856,30 +856,47 @@ def gwas_with_redis(key,species,new_code=True): def narray(t): info("Type is "+t) - v = params[t] + v = params.get(t) if v is not None: - v = np.array(v).astype(np.float) - print(v) + # Note input values can be array of string or float + v1 = [x if x != 'NA' else 'nan' for x in v] + v = np.array(v1).astype(np.float) return v - def narrayT(t): - m = narray(t) + def marray(t): + info("Type is "+t) + v = params.get(t) + if v is not None: + m = [] + for r in v: + # Note input values can be array of string or float + r1 = [x if x != 'NA' else 'nan' for x in r] + m.append(np.array(r1).astype(np.float)) + return np.array(m) + return np.array(v) + + def marrayT(t): + m = marray(t) if m is not None: return m.T return m # We are transposing before we enter run_gwas - this should happen on the webserver # side (or when reading data from file) - print(params) - k = narray('kinship_matrix') - g = narrayT('genotype_matrix') + k = marray('kinship_matrix') + g = marrayT('genotype_matrix') + mprint("geno",g) y = narray('pheno_vector') n = len(y) - m = params['num_genotypes'] - ps,ts = run_gwas(species,n,m,k,y,g,narray('covariate_matrix'),params['restricted_max_likelihood'],params['refit'],params['input_file_name'],new_code) + m = params.get('num_genotypes') + if m is None: + m = g.shape[0] + info("m=%d,n=%d" % (m,n)) + ps,ts = run_gwas(species,n,m,k,y,g,narray('covariate_matrix'),params['restricted_max_likelihood'],params['refit'],params.get('input_file_name'),new_code) results_key = "pylmm:results:" + params['temp_uuid'] + # fatal(results_key) json_results = json.dumps(dict(p_values = ps, t_stats = ts)) |