diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 24 |
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!") |