Added file that checks how much time is added to a loop's runtime by print statements

Continued work on file that processes each individual chunk of the snp iterator/plink input

2 files changed, 48 insertions, 1 deletions

diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
new file mode 100644
index 00000000..540e0904
--- /dev/null
+++ b/wqflask/maintenance/print_benchmark.py
@@ -0,0 +1,43 @@
+#!/usr/bin/python
+
+from __future__ import absolute_import, print_function, division
+
+import time
+
+from pprint import pformat as pf
+
+
+class TheCounter(object):
+    Counters = {}
+    
+    def __init__(self):
+        start_time = time.time()
+        for counter in range(170000):
+            self.print_it(counter)
+        self.time_took = time.time() - start_time
+        TheCounter.Counters[self.__class__.__name__] = self.time_took        
+
+class PrintAll(TheCounter): 
+    def print_it(self, counter):
+        print(counter)
+        
+class PrintSome(TheCounter):
+    def print_it(self, counter):
+        if counter % 1000 == 0:
+            print(counter)
+            
+class PrintNone(TheCounter):
+    def print_it(self, counter):
+        pass
+    
+    
+def new_main():
+    print("Running new_main")
+    tests = [PrintAll, PrintSome, PrintNone]
+    for test in tests:
+        test()
+        
+    print(pf(TheCounter.Counters))
+
+if __name__ == '__main__':
+    new_main()
\ No newline at end of file
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/process_plink.py b/wqflask/wqflask/my_pylmm/pyLMM/process_plink.py
index 5ce7adbc..8f7ad243 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/process_plink.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/process_plink.py
@@ -13,6 +13,9 @@ plink_pickled = Redis.lpop("plink_inputs")
 
 plink_data = pickle.loads(plink_pickled)
 
+identifier = plink_data['identifier']
+print("identifier: ", identifier)
+
 
 ps, ts = lmm.human_association(snp,
                                 n,
@@ -21,4 +24,5 @@ ps, ts = lmm.human_association(snp,
                                 pheno_vector,
                                 covariate_matrix,
                                 kinship_matrix,
-                                refit)
\ No newline at end of file
+                                refit)
+