diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 26 |
1 files changed, 19 insertions, 7 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 69a80411..627cc7a4 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -21,8 +21,8 @@ from optparse import OptionParser import sys import tsvreader import numpy as np -from lmm import gn2_load_redis -from kinship import kinship +from lmm import gn2_load_redis, calculate_kinship +from kinship import kinship, kinship_full from genotype import normalizeGenotype from phenotype import removeMissingPhenotypes @@ -106,10 +106,22 @@ if cmd == 'redis': assert(options.testing and round(ps[-1],4)==0.3461) elif cmd == 'kinship': gn = [] - for snp in G.T: - gn.append( normalizeGenotype(snp) ) - G2 = np.array(gn) - print G2.shape,G2 - K = kinship(G2,options) + for ind_g in g: + if len(gn)>=8000: break + gn.append( normalizeGenotype(ind_g) ) + K = kinship_full(np.array(gn),options) + print "first Kinship method",K.shape,K + K = kinship(np.array(gn),options) + print "second Kinship method",K.shape,K + sys.exit(1) + gnt = np.array(gn).T + Y,g = removeMissingPhenotypes(y,gnt,options.verbose) + G = g + print G.shape,G + K = calculate_kinship(np.copy(G),None,options) + print G.shape,G + print "first Kinship method",K.shape,K + K = kinship(G.T,options) + assert(K[0][0]==1.28) else: print "Doing nothing" |