diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 34 |
1 files changed, 19 insertions, 15 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 07b55726..6e22e6c9 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -805,7 +805,7 @@ class LMM: pl.title(title) -def gn2_redis(key,species,new_code=True): +def gwas_using_redis(key,species,new_code=True): """ Invoke pylmm using Redis as a container. new_code runs the new version @@ -861,18 +861,6 @@ def gn2_redis(key,species,new_code=True): Redis.expire(results_key, 60*60) return ps, ts -# This is the main function used by Genenetwork2 (with environment) -def gn2_main(): - parser = argparse.ArgumentParser(description='Run pyLMM') - parser.add_argument('-k', '--key') - parser.add_argument('-s', '--species') - - opts = parser.parse_args() - - key = opts.key - species = opts.species - - gn2_redis(key,species) def gn2_load_redis(key,species,kinship,pheno,geno,new_code=True): """ @@ -898,7 +886,7 @@ def gn2_load_redis(key,species,kinship,pheno,geno,new_code=True): Redis.set(key, json_params) Redis.expire(key, 60*60) - return gn2_redis(key,species,new_code) + return gwas_using_redis(key,species,new_code) def gn2_iter_redis(key,species,kinship,pheno,geno_iterator): """ @@ -925,7 +913,23 @@ def gn2_iter_redis(key,species,kinship,pheno,geno_iterator): Redis.set(key, json_params) Redis.expire(key, 60*60) - return gn2_redis(key,species,new_code) + return gwas_using_redis(key,species,new_code) + +# This is the main function used by Genenetwork2 (with environment) +# +# Note that this calling route will become OBSOLETE (we should use runlmm.py +# instead) +def gn2_main(): + parser = argparse.ArgumentParser(description='Run pyLMM') + parser.add_argument('-k', '--key') + parser.add_argument('-s', '--species') + + opts = parser.parse_args() + + key = opts.key + species = opts.species + + gwas_using_redis(key,species) if __name__ == '__main__': |