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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/kinship.py2
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/runlmm.py19
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