From 24b44a2de4fb47c2ed6a6a3def3acce1c06bebf4 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 14 Mar 2015 15:26:07 +0300
Subject: Conditional run of K calculation

---
 wqflask/wqflask/my_pylmm/pyLMM/kinship.py |  2 +-
 wqflask/wqflask/my_pylmm/pyLMM/runlmm.py  | 19 ++++++++++---------
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
index c1750e1d..1dca1c57 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/kinship.py
@@ -59,7 +59,7 @@ def compute_matrixMult(job,W,q = None):
 def f_init(q):
     compute_matrixMult.q = q
 
-def kinship_full(G,options):
+def kinship_full(G):
     print G.shape
     m = G.shape[0] # snps
     n = G.shape[1] # inds
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index 21d9240b..26485136 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -139,20 +139,21 @@ elif cmd == 'kinship':
         print "MAF replacements: \n",G
     if not options.skip_genotype_normalization:
         G = np.apply_along_axis( genotype.normalize, axis=1, arr=G)
-            
-    K = kinship_full(G,options)
-    print "Genotype",G.shape, "\n", G
-    print "first Kinship method",K.shape,"\n",K
-    K2 = calculate_kinship(np.copy(G.T),temp_data=None)
-    print "Genotype",G.shape, "\n", G
-    print "GN2 Kinship method",K2.shape,"\n",K2
 
+    if True:
+        K = kinship_full(G)
+        print "Genotype",G.shape, "\n", G
+        print "first Kinship method",K.shape,"\n",K
+        k1 = round(K[0][0],4)
+        K2 = calculate_kinship(np.copy(G.T),temp_data=None)
+        print "Genotype",G.shape, "\n", G
+        print "GN2 Kinship method",K2.shape,"\n",K2
+        k2 = round(K2[0][0],4)
+    
     print "Genotype",G.shape, "\n", G
     K3 = kinship(np.copy(G),options)
     print "third Kinship method",K3.shape,"\n",K3
     sys.stderr.write(options.geno+"\n")
-    k1 = round(K[0][0],4)
-    k2 = round(K2[0][0],4)
     k3 = round(K3[0][0],4)
     if options.geno == 'data/small.geno':
         assert k1==0.7939, "k1=%f" % k1
-- 
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