diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/kinship.py | 5 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm2.py | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/standalone.py | 9 |
4 files changed, 18 insertions, 10 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py index 43e7fe36..d3792570 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py @@ -155,13 +155,12 @@ def kinship(G,computeSize=1000,numThreads=None,useBLAS=False,verbose=True): # np.savetxt(outFile+".kve",Kve) return K -def kvakve(K, callbacks): +def kvakve(K, uses): """ Obtain eigendecomposition for K and return Kva,Kve where Kva is cleaned of small values < 1e-6 (notably smaller than zero) """ - info = callbacks()['info'] - mprint = callbacks()['mprint'] + info,mprint = uses('info','mprint') info("Obtaining eigendecomposition for %dx%d matrix" % (K.shape[0],K.shape[1]) ) Kva,Kve = linalg.eigh(K) diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 5ad644e2..2076bc84 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -57,11 +57,11 @@ import gwas # ---- A trick to decide on the environment: try: from wqflask.my_pylmm.pyLMM import chunks - from gn2 import callbacks + from gn2 import uses except ImportError: print("WARNING: Standalone version missing the Genenetwork2 environment\n") has_gn2=False - from standalone import callbacks + from standalone import uses pass #np.seterr('raise') @@ -597,7 +597,7 @@ class LMM: # if self.verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) ) begin = time.time() # Kva,Kve = linalg.eigh(K) - Kva,Kve = kvakve(K,callbacks) + Kva,Kve = kvakve(K,uses) end = time.time() if self.verbose: sys.stderr.write("Total time: %0.3f\n" % (end - begin)) print("sum(Kva),sum(Kve)=",sum(Kva),sum(Kve)) diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py index 6aefb9d3..5b93ae0d 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm2.py @@ -24,14 +24,14 @@ from scipy import optimize from optmatrix import matrixMult import kinship -# A trick to decide on the environment: +# ---- A trick to decide on the environment: try: from wqflask.my_pylmm.pyLMM import chunks - from gn2 import callbacks + from gn2 import uses except ImportError: print("WARNING: Standalone version missing the Genenetwork2 environment\n") has_gn2=False - from standalone import callbacks + from standalone import uses pass def calculateKinship(W,center=False): @@ -194,7 +194,7 @@ class LMM2: # if self.verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) ) begin = time.time() # Kva,Kve = linalg.eigh(K) - Kva,Kve = kinship.kvakve(K,callbacks) + Kva,Kve = kinship.kvakve(K,uses) end = time.time() if self.verbose: sys.stderr.write("Total time: %0.3f\n" % (end - begin)) print("sum(Kva),sum(Kve)=",sum(Kva),sum(Kve)) diff --git a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py index bbee3cd7..705da21f 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py @@ -44,6 +44,12 @@ def callbacks(): progress = progress, mprint = mprint ) + +def uses(*funcs): + """ + Some sugar + """ + return [callbacks()[func] for func in funcs] # ----- Minor test cases: @@ -69,3 +75,6 @@ if __name__ == '__main__': [5,0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15], [6,0.5,0.6096595 , -0.31559815, -0.52793285, 1.16573418e-15]] mprint("matrix",matrix) + ix,dx = uses("info","debug") + ix("ix") + dx("dx") |