diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 17 |
1 files changed, 15 insertions, 2 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 3801529e..f095bb73 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, gn2_load_redis_iter, calculate_kinship_new +from lmm import gn2_load_redis, gn2_load_redis_iter, calculate_kinship_new, run_gwas from kinship import kinship, kinship_full import genotype import phenotype @@ -103,7 +103,20 @@ if options.geno and cmd != 'iterator': g = tsvreader.geno(options.geno) print g.shape -if cmd == 'iterator': +if cmd == 'run': + if options.remove_missing_phenotypes: + raise Exception('Can not use --remove-missing-phenotypes with LMM2') + snp_iterator = tsvreader.geno_iter(options.geno) + n = len(y) + m = g.shape[1] + ps, ts = run_gwas('other',n,m,k,y,g.T) + print np.array(ps) + print len(ps),sum(ps) + # Test results + p1 = round(ps[0],4) + p2 = round(ps[-1],4) + +elif cmd == 'iterator': if options.remove_missing_phenotypes: raise Exception('Can not use --remove-missing-phenotypes with LMM2') snp_iterator = tsvreader.geno_iter(options.geno) |