From 31dc2a62727d14e0eab154a1e2400fd7cf587b42 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 15 Mar 2015 14:25:07 +0300
Subject: A little cleanup

---
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py    | 5 ++---
 wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 4 +++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index bfb95045..5aa27106 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -333,8 +333,8 @@ def calculate_kinship_new(genotype_matrix, temp_data=None):
     Call the new kinship calculation where genotype_matrix contains
     inds (columns) by snps (rows).
     """
-    G = np.apply_along_axis( genotype.normalize, axis=1, arr=genotype_matrix.T)
-    return kinship(G),G.T
+    G = np.apply_along_axis( genotype.normalize, axis=0, arr=genotype_matrix)
+    return kinship(G.T),G
 
 def calculate_kinship_old(genotype_matrix, temp_data=None):
     """
@@ -749,7 +749,6 @@ def gn2_redis(key,species):
     print('pheno', np.array(params['pheno_vector']))
     geno = np.array(params['genotype_matrix'])
     print('geno', geno.shape, geno)
-    # sys.exit(1)
     
     if species == "human" :
         ps, ts = run_human(pheno_vector = np.array(params['pheno_vector']),
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index 469ba6c9..6bb79856 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -116,7 +116,9 @@ if cmd == 'redis':
     g = None
     gnt = None
 
-    ps, ts = gn2_load_redis('testrun','other',k,Y,G.T)
+    gt = G.T
+    G = None
+    ps, ts = gn2_load_redis('testrun','other',k,Y,gt)
     print np.array(ps)
     # Test results
     p1 = round(ps[0],4)
-- 
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