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authorPjotr Prins2015-03-14 12:29:35 +0300
committerPjotr Prins2015-03-14 12:29:35 +0300
commit0533dc4c053165853faa0512229eef30a174c425 (patch)
tree2ebfadcba709481a995fa3b6aa53a9d8cb50b413 /wqflask
parent2c6d1fcba1138415ecb3ca447e09d06d660af0db (diff)
downloadgenenetwork2-0533dc4c053165853faa0512229eef30a174c425.tar.gz
Removing all references to is_testing
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py24
1 files changed, 10 insertions, 14 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 7bf77be5..87b999e8 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -255,8 +255,8 @@ def run_other(pheno_vector,
genotype_matrix,
restricted_max_likelihood=True,
refit=False,
- tempdata=None, # <---- can not be None
- is_testing=False):
+ tempdata=None # <---- can not be None
+ ):
"""Takes the phenotype vector and genotype matrix and returns a set of p-values and t-statistics
@@ -268,9 +268,9 @@ def run_other(pheno_vector,
"""
print("In run_other")
- print("REML=",restricted_max_likelihood," REFIT=",refit, "TESTING=",is_testing)
+ print("REML=",restricted_max_likelihood," REFIT=",refit)
with Bench("Calculate Kinship"):
- kinship_matrix = calculate_kinship(genotype_matrix, tempdata, is_testing)
+ kinship_matrix = calculate_kinship(genotype_matrix, tempdata)
print("kinship_matrix: ", pf(kinship_matrix))
print("kinship_matrix.shape: ", pf(kinship_matrix.shape))
@@ -326,7 +326,7 @@ def matrixMult(A,B):
return linalg.fblas.dgemm(alpha=1.,a=AA,b=BB,trans_a=transA,trans_b=transB)
-def calculate_kinship(genotype_matrix, temp_data=None, is_testing=False):
+def calculate_kinship(genotype_matrix, temp_data=None):
"""
genotype_matrix is an n x m matrix encoding SNP minor alleles.
@@ -340,8 +340,6 @@ def calculate_kinship(genotype_matrix, temp_data=None, is_testing=False):
print("genotype 2D matrix m (snps) is:", m)
keep = []
for counter in range(m):
- # if is_testing and counter>8:
- # break
#print("type of genotype_matrix[:,counter]:", pf(genotype_matrix[:,counter]))
#Checks if any values in column are not numbers
not_number = np.isnan(genotype_matrix[:,counter])
@@ -490,7 +488,7 @@ class LMM:
is not done consistently.
"""
- def __init__(self,Y,K,Kva=[],Kve=[],X0=None,verbose=True,is_testing=False):
+ def __init__(self,Y,K,Kva=[],Kve=[],X0=None,verbose=True):
"""
The constructor takes a phenotype vector or array of size n.
@@ -500,7 +498,6 @@ class LMM:
When this parameter is not provided, the constructor will set X0 to an n x 1 matrix of all ones to represent a mean effect.
"""
- self.is_testing = True
if X0 == None: X0 = np.ones(len(Y)).reshape(len(Y),1)
self.verbose = verbose
@@ -728,7 +725,7 @@ class LMM:
pl.title(title)
-def gn2_redis(key,species,is_testing=False):
+def gn2_redis(key,species):
json_params = Redis.get(key)
params = json.loads(json_params)
@@ -753,8 +750,7 @@ def gn2_redis(key,species,is_testing=False):
genotype_matrix = geno,
restricted_max_likelihood = params['restricted_max_likelihood'],
refit = params['refit'],
- tempdata = tempdata,
- is_testing=is_testing)
+ tempdata = tempdata)
results_key = "pylmm:results:" + params['temp_uuid']
@@ -779,7 +775,7 @@ def gn2_main():
gn2_redis(key,species)
-def gn2_load_redis(key,species,kinship,pheno,geno,is_testing):
+def gn2_load_redis(key,species,kinship,pheno,geno):
print("Loading Redis from parsed data")
params = dict(pheno_vector = pheno.tolist(),
genotype_matrix = geno.tolist(),
@@ -796,7 +792,7 @@ def gn2_load_redis(key,species,kinship,pheno,geno,is_testing):
Redis.set(key, json_params)
Redis.expire(key, 60*60)
- return gn2_redis(key,species,is_testing)
+ return gn2_redis(key,species)
if __name__ == '__main__':
print("WARNING: Calling pylmm from lmm.py will become OBSOLETE, use runlmm.py instead!")