diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 65 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 4 |
2 files changed, 38 insertions, 31 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index b8650938..88ca6a7f 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -805,6 +805,36 @@ class LMM: pl.title(title) +def gwas_without_redis(species,k,y,geno,cov,reml,refit,inputfn,new_code): + """ + Invoke pylmm using a genotype (SNP) iterator + """ + info("gwas_without_redis") + print('pheno', y) + + if species == "human" : + print('kinship', k ) + ps, ts = run_human(pheno_vector = y, + covariate_matrix = cov, + plink_input_file = inputfn, + kinship_matrix = k, + refit = refit, tempdata=tempdata) + else: + print('geno', geno.shape, geno) + + if new_code: + ps, ts = run_other_new(pheno_vector = y, + genotype_matrix = geno, + restricted_max_likelihood = reml, + refit = refit, + tempdata = tempdata) + else: + ps, ts = run_other_old(pheno_vector = y, + genotype_matrix = geno, + restricted_max_likelihood = reml, + refit = refit, + tempdata = tempdata) + def gwas_using_redis(key,species,new_code=True): """ Invoke pylmm using Redis as a container. new_code runs the new @@ -823,33 +853,7 @@ def gwas_using_redis(key,species,new_code=True): debug("Updating REDIS percent_complete=%d" % (round(i*100.0/total))) progress_set_func(update_tempdata) - - print('pheno', np.array(params['pheno_vector'])) - - if species == "human" : - print('kinship', np.array(params['kinship_matrix'])) - ps, ts = run_human(pheno_vector = np.array(params['pheno_vector']), - covariate_matrix = np.array(params['covariate_matrix']), - plink_input_file = params['input_file_name'], - kinship_matrix = np.array(params['kinship_matrix']), - refit = params['refit'], - tempdata = tempdata) - else: - geno = np.array(params['genotype_matrix']) - print('geno', geno.shape, geno) - - if new_code: - ps, ts = run_other_new(pheno_vector = np.array(params['pheno_vector']), - genotype_matrix = geno, - restricted_max_likelihood = params['restricted_max_likelihood'], - refit = params['refit'], - tempdata = tempdata) - else: - ps, ts = run_other_old(pheno_vector = np.array(params['pheno_vector']), - genotype_matrix = geno, - restricted_max_likelihood = params['restricted_max_likelihood'], - refit = params['refit'], - tempdata = tempdata) + ps,ts = gwas_without_redis(species,np.array(params['kinship_matrix']),np.array(params['pheno_vector']),np.array(params['genotype_matrix']),np.array(params['covariate_matrix']),params['restricted_max_likelihood'],params['refit'],params['input_file_name'],new_code) results_key = "pylmm:results:" + params['temp_uuid'] @@ -874,6 +878,8 @@ def gn2_load_redis(key,species,kinship,pheno,geno,new_code=True): params = dict(pheno_vector = pheno.tolist(), genotype_matrix = geno.tolist(), kinship_matrix = k, + covariate_matrix = None, + input_file_name = None, restricted_max_likelihood = True, refit = False, temp_uuid = "testrun_temp_uuid", @@ -888,7 +894,7 @@ def gn2_load_redis(key,species,kinship,pheno,geno,new_code=True): return gwas_using_redis(key,species,new_code) -def gn2_iter_redis(key,species,kinship,pheno,geno_iterator): +def gn2_load_redis_iter(key,species,kinship,pheno,geno_iterator): """ This function emulates GN2 behaviour by pre-loading Redis with a SNP iterator, for this it sets a key for every genotype (SNP) @@ -907,6 +913,8 @@ def gn2_iter_redis(key,species,kinship,pheno,geno_iterator): genotype_matrix = "iterator", genotypes = i, kinship_matrix = k, + covariate_matrix = None, + input_file_name = None, restricted_max_likelihood = True, refit = False, temp_uuid = "testrun_temp_uuid", @@ -918,7 +926,6 @@ def gn2_iter_redis(key,species,kinship,pheno,geno_iterator): json_params = json.dumps(params) Redis.set(key, json_params) Redis.expire(key, 60*60) - return gwas_using_redis(key,species) # This is the main function used by Genenetwork2 (with environment) diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 3b0672b4..ab698e41 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -21,7 +21,7 @@ from optparse import OptionParser import sys import tsvreader import numpy as np -from lmm import gn2_load_redis, gn2_iter_redis, calculate_kinship_new +from lmm import gn2_load_redis, gn2_load_redis_iter, calculate_kinship_new from kinship import kinship, kinship_full import genotype import phenotype @@ -107,7 +107,7 @@ if 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_iter_redis('testrun_iter','other',k,y,snp_iterator) + ps, ts = gn2_load_redis_iter('testrun_iter','other',k,y,snp_iterator) print np.array(ps) print len(ps),sum(ps) # Test results |