From 3cff3091379a2e8835027c272ada0d8d4314624e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 16 Mar 2015 13:15:21 +0300
Subject: Output added

---
 wqflask/wqflask/my_pylmm/pyLMM/kinship.py |  4 ++--
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py     | 16 +++++++++-------
 wqflask/wqflask/my_pylmm/pyLMM/runlmm.py  |  1 +
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
index bb4f5ace..cd2445f1 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
@@ -164,8 +164,8 @@ def kvakve(K, verbose=True):
    
    Kva,Kve = linalg.eigh(K)
    if verbose:
-      print("self.Kva is: ", Kva.shape, Kva)
-      print("self.Kve is: ", Kve.shape, Kve)
+      print("Kva is: ", Kva.shape, Kva)
+      print("Kve is: ", Kve.shape, Kve)
 
    if sum(Kva < 1e-6):
       if verbose: sys.stderr.write("Cleaning %d eigen values\n" % (sum(Kva < 1e-6)))
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 17fe952a..9fd05b42 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -533,11 +533,12 @@ class LMM:
        
        if len(Kva) == 0 or len(Kve) == 0:
           # if self.verbose: sys.stderr.write("Obtaining eigendecomposition for %dx%d matrix\n" % (K.shape[0],K.shape[1]) )
-          # begin = time.time()
+          begin = time.time()
           # Kva,Kve = linalg.eigh(K)
-          # end = time.time()
-          # if self.verbose: sys.stderr.write("Total time: %0.3f\n" % (end - begin))
           Kva,Kve = kvakve(K)
+          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))
 
        self.K = K
        self.Kva = Kva
@@ -547,10 +548,11 @@ class LMM:
        self.Y = Y
        self.X0 = X0
        self.N = self.K.shape[0]
- 
-       if sum(self.Kva < 1e-6):
-          if self.verbose: sys.stderr.write("Cleaning %d eigen values\n" % (sum(self.Kva < 0)))
-          self.Kva[self.Kva < 1e-6] = 1e-6
+
+       # ----> Below moved to kinship.kvakve(K)
+       # if sum(self.Kva < 1e-6):
+       #    if self.verbose: sys.stderr.write("Cleaning %d eigen values\n" % (sum(self.Kva < 0)))
+       #    self.Kva[self.Kva < 1e-6] = 1e-6
  
        self.transform()
 
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index 6bb79856..cef0cdc4 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -120,6 +120,7 @@ if cmd == 'redis':
     G = None
     ps, ts = gn2_load_redis('testrun','other',k,Y,gt)
     print np.array(ps)
+    print sum(ps)
     # Test results
     p1 = round(ps[0],4)
     p2 = round(ps[-1],4)
-- 
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