diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 8 |
1 files changed, 4 insertions, 4 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index cef0cdc4..f17f1bd1 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -21,7 +21,7 @@ from optparse import OptionParser import sys import tsvreader import numpy as np -from lmm import gn2_load_redis, calculate_kinship +from lmm import gn2_load_redis, calculate_kinship_old from kinship import kinship, kinship_full import genotype import phenotype @@ -151,17 +151,17 @@ elif cmd == 'kinship': gnt = None if options.test_kinship: - K = kinship_full(G) + K = kinship_full(np.copy(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) + K2,G = calculate_kinship_old(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) + K3 = kinship(G.T) print "third Kinship method",K3.shape,"\n",K3 sys.stderr.write(options.geno+"\n") k3 = round(K3[0][0],4) |