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authorPjotr Prins2015-03-20 12:18:03 +0300
committerPjotr Prins2015-03-20 12:18:03 +0300
commit38594c7781b587a24be14b9631a73662ee3fdc2b (patch)
tree85c363ccc3127c6245a7984f32b8c4688ec60f66 /wqflask
parent8e9d7cde41800766fec835ca0c4a55c6327e05c8 (diff)
downloadgenenetwork2-38594c7781b587a24be14b9631a73662ee3fdc2b.tar.gz
Fall back on calculate_kinship_new again
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py2
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/runlmm.py2
2 files changed, 2 insertions, 2 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index c040e3c2..a649029c 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -277,7 +277,7 @@ def run_other_old(pheno_vector,
print("Running the original LMM engine in run_other (old)")
print("REML=",restricted_max_likelihood," REFIT=",refit)
with Bench("Calculate Kinship"):
- kinship_matrix,genotype_matrix = calculate_kinship_old(genotype_matrix, tempdata)
+ kinship_matrix,genotype_matrix = calculate_kinship_new(genotype_matrix, tempdata)
print("kinship_matrix: ", pf(kinship_matrix))
print("kinship_matrix.shape: ", pf(kinship_matrix.shape))
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index 6a38da56..88e2a033 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -184,7 +184,7 @@ elif cmd == 'kinship':
gnt = None
if options.test_kinship:
- K = kinship_full(np.copy(G))
+ K = kinship_full(np.copy(G),uses)
print "Genotype",G.shape, "\n", G
print "first Kinship method",K.shape,"\n",K
k1 = round(K[0][0],4)