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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py65
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/runlmm.py4
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