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-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py2
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py5
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