diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/lmm.py | 49 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 11 |
2 files changed, 42 insertions, 18 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py index 3cbab149..8c6e30e8 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py @@ -719,23 +719,11 @@ class LMM: pl.ylabel("Probability of data") pl.title(title) -# 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 - + +def gn2_redis(key,species): json_params = Redis.get(key) params = json.loads(json_params) - #print("params:", params) - - #print("kinship_matrix:", params['kinship_matrix']) tempdata = temp_data.TempData(params['temp_uuid']) if species == "human" : @@ -760,7 +748,38 @@ def gn2_main(): #Pushing json_results into a list where it is the only item because blpop needs a list Redis.rpush(results_key, json_results) Redis.expire(results_key, 60*60) - + +# 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): + print("Loading Redis from parsed data") + params = dict(pheno_vector = pheno.tolist(), + genotype_matrix = geno.tolist(), + restricted_max_likelihood = True, + refit = False, + temp_uuid = "testrun_temp_uuid", + + # meta data + timestamp = datetime.datetime.now().isoformat(), + ) + + json_params = json.dumps(params) + Redis.set(key, json_params) + Redis.expire(key, 60*60) + + gn2_redis(key,species) + if __name__ == '__main__': print("WARNING: Calling pylmm from lmm.py will become OBSOLETE, use runlmm.py instead!") if has_gn2: diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index bed2e39e..525c43fc 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -19,6 +19,7 @@ from optparse import OptionParser import tsvreader +from lmm import gn2_load_redis usage = """ python runlmm.py [options] command @@ -29,6 +30,7 @@ python runlmm.py [options] command Current commands are: parse : only parse input files + redis : use Redis to call into GN2 try --help for more information """ @@ -58,12 +60,15 @@ print "Command: ",cmd if options.kinship: k = tsvreader.kinship(options.kinship) - print len(k) + print k.shape if options.pheno: y = tsvreader.pheno(options.pheno) - print len(y) + print y.shape if options.geno: g = tsvreader.geno(options.geno) - print len(g) + print g.shape + +if cmd == 'redis': + gn2_load_redis('testrun','other',k,y,g.T) |