diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 6 |
1 files changed, 2 insertions, 4 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 036bf7d5..3b0672b4 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_new +from lmm import gn2_load_redis, gn2_iter_redis, calculate_kinship_new from kinship import kinship, kinship_full import genotype import phenotype @@ -104,11 +104,9 @@ if options.geno and cmd != 'iterator': print g.shape if cmd == 'iterator': - def snp_iterator(func): - tsvreader.geno_iter(options.geno,func) - if options.remove_missing_phenotypes: raise Exception('Can not use --remove-missing-phenotypes with LMM2') + snp_iterator = tsvreader.geno_iter(options.geno) ps, ts = gn2_iter_redis('testrun_iter','other',k,y,snp_iterator) print np.array(ps) print len(ps),sum(ps) |