aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py49
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/runlmm.py11
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)