From 4ad55a0ebc1fc77da8e9aa6ec565b2b10c373e9b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 6 Apr 2015 21:30:13 +0000
Subject: Just committing a couple minor bug fixes to get code working after
 pulling Pjotr's latest changes

---
 wqflask/wqflask/marker_regression/marker_regression.py | 2 +-
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py                  | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 3fb9915b..7708356b 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -701,7 +701,7 @@ class MarkerRegression(object):
             no_val_samples = self.identify_empty_samples()
             trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
             
-            genotype_matrix = np.array(trimmed_genotype_data).T
+            genotype_matrix = np.array(genotype_data).T
 
             #print("pheno_vector: ", pf(pheno_vector))
             #print("genotype_matrix: ", pf(genotype_matrix))
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 58ff809b..53689071 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -43,13 +43,14 @@ Redis = Redis()
 
 import sys
 sys.path.append("/home/zas1024/gene/wqflask/")
-sys.path.append("/home/danny/GeneNetwork/wqflask/wqflask/my_pylmm/pyLMM/")
-print("sys.path2:", sys.path)
 
 has_gn2=True
 
 from utility.benchmark import Bench
 from utility import temp_data
+
+sys.path.append("/home/zas1024/gene/wqflask/wqflask/my_pylmm/pyLMM/")
+
 from kinship import kinship, kinship_full, kvakve
 import genotype
 import phenotype
-- 
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