diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 28 |
2 files changed, 22 insertions, 13 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 87b999e8..d6830787 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -338,6 +338,7 @@ def calculate_kinship(genotype_matrix, temp_data=None): m = genotype_matrix.shape[1] print("genotype 2D matrix n (inds) is:", n) print("genotype 2D matrix m (snps) is:", m) + assert m>n, "n should be larger than m (snps>inds)" keep = [] for counter in range(m): #print("type of genotype_matrix[:,counter]:", pf(genotype_matrix[:,counter])) @@ -777,9 +778,13 @@ def gn2_main(): def gn2_load_redis(key,species,kinship,pheno,geno): print("Loading Redis from parsed data") + if kinship == None: + k = None + else: + k = kinship.tolist() params = dict(pheno_vector = pheno.tolist(), genotype_matrix = geno.tolist(), - kinship_matrix= kinship.tolist(), + kinship_matrix= k, restricted_max_likelihood = True, refit = False, temp_uuid = "testrun_temp_uuid", diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 80478368..7a77ad0a 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -98,16 +98,20 @@ if options.geno: if cmd == 'redis': # Emulating the redis setup of GN2 - gn = [] - for ind_g in g: - gn.append( genotype.normalize(ind_g) ) - gnt = np.array(gn).T - if y: - Y,G = phenotype.remove_missing(y,gnt,options.verbose) - print "G",G.shape,G - else: - G = gnt - ps, ts = gn2_load_redis('testrun','other',k,Y,G,options.testing) + G = g + print "Original G",G.shape, "\n", G + if y != None: + gnt = np.array(g).T + Y,g = phenotype.remove_missing(y,g.T,options.verbose) + G = g.T + print "Removed missing phenotypes",G.shape, "\n", G + if options.maf_normalization: + G = np.apply_along_axis( genotype.replace_missing_with_MAF, axis=0, arr=g ) + print "MAF replacements: \n",G + if not options.skip_genotype_normalization: + G = np.apply_along_axis( genotype.normalize, axis=1, arr=G) + + ps, ts = gn2_load_redis('testrun','other',k,Y,G.T) print np.array(ps) print round(ps[0],4) assert(options.testing and round(ps[0],4)==0.7262) @@ -116,8 +120,8 @@ if cmd == 'redis': elif cmd == 'kinship': G = g print "Original G",G.shape, "\n", G - if y: - gnt = np.array(gn).T + if y != None: + gnt = np.array(g).T Y,g = phenotype.remove_missing(y,g.T,options.verbose) G = g.T print "Removed missing phenotypes",G.shape, "\n", G |