diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 9 |
1 files changed, 7 insertions, 2 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index ef0bdd7e..5a4bd268 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -99,11 +99,16 @@ if options.pheno: y = tsvreader.pheno(options.pheno) print y.shape -if options.geno: +if options.geno and cmd != 'iterator': g = tsvreader.geno(options.geno) print g.shape -if cmd == 'redis_new': +if cmd == 'iterator': + print "ITERATE over SNPs" + def pretty(snpid,values): + print snpid,values + print tsvreader.geno_iter(options.geno,pretty) +elif cmd == 'redis_new': # The main difference between redis_new and redis is that missing # phenotypes are handled by the first if options.remove_missing_phenotypes: |