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authorPjotr Prins2015-03-14 16:52:47 +0300
committerPjotr Prins2015-03-14 16:52:47 +0300
commitc784f2fb2e3e4ad6cb6d6425aa7ec1596c2bd132 (patch)
tree71200c71e2ed5f5812dee1708701bf5944209cd9 /wqflask
parent58f43e9e767890031c77e44d10939c48bc1c81fe (diff)
downloadgenenetwork2-c784f2fb2e3e4ad6cb6d6425aa7ec1596c2bd132.tar.gz
Allow queue to be 2xCPU. Disable output files
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/kinship.py24
1 files changed, 12 insertions, 12 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
index 967eca81..1383c782 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
@@ -71,7 +71,6 @@ def compute_matrixMult(job,W,q = None):
def f_init(q):
compute_matrixMult.q = q
-
# Calculate the kinship matrix from G (SNPs as rows!), returns K
#
def kinship(G,options):
@@ -119,7 +118,7 @@ def kinship(G,options):
# Multi-core
results.append(p.apply_async(compute_matrixMult, (job,W)))
# Do we have a result?
- while (len(results)-completed>cpu_num):
+ while (len(results)-completed>cpu_num*2):
try:
j,x = q.get_nowait()
if options.verbose: sys.stderr.write("Job "+str(j)+" finished\n")
@@ -141,16 +140,17 @@ def kinship(G,options):
completed += 1
K = K / float(snps)
- outFile = 'runtest.kin'
- if options.verbose: sys.stderr.write("Saving Kinship file to %s\n" % outFile)
- np.savetxt(outFile,K)
-
- if options.saveKvaKve:
- if options.verbose: sys.stderr.write("Obtaining Eigendecomposition\n")
- Kva,Kve = linalg.eigh(K)
- if options.verbose: sys.stderr.write("Saving eigendecomposition to %s.[kva | kve]\n" % outFile)
- np.savetxt(outFile+".kva",Kva)
- np.savetxt(outFile+".kve",Kve)
+
+ # outFile = 'runtest.kin'
+ # if options.verbose: sys.stderr.write("Saving Kinship file to %s\n" % outFile)
+ # np.savetxt(outFile,K)
+
+ # if options.saveKvaKve:
+ # if options.verbose: sys.stderr.write("Obtaining Eigendecomposition\n")
+ # Kva,Kve = linalg.eigh(K)
+ # if options.verbose: sys.stderr.write("Saving eigendecomposition to %s.[kva | kve]\n" % outFile)
+ # np.savetxt(outFile+".kva",Kva)
+ # np.savetxt(outFile+".kve",Kve)
return K