From 6b8321d77e915dc5aec0c272c1cb84c2af3e6191 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 18 Mar 2015 12:17:59 +0300
Subject: Replace progress meter

---
 wqflask/wqflask/my_pylmm/pyLMM/gn2.py        |  7 ++++++-
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py        | 17 ++++++-----------
 wqflask/wqflask/my_pylmm/pyLMM/standalone.py |  2 +-
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/gn2.py b/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
index c71b9f22..f8033ac5 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/gn2.py
@@ -12,11 +12,16 @@ import logging
 # logging.basicConfig(level=logging.DEBUG)
 # np.set_printoptions()
 
+def set_progress_storage(location):
+    global storage
+    storage = location
+    
 def progress(location, count, total):
     """
     Progress update
     """
-    logging.info("Progress: %s %d%%" % (location,round(count*100.0/total)))
+    storage.store("percent_complete",round(count*100.0)/total)
+    logger.info("Progress: %s %d%%" % (location,round(count*100.0/total)))
 
 def mprint(msg,data):
     """
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 95272818..eab7d91d 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -65,6 +65,8 @@ except ImportError:
     sys.stderr.write("WARNING: LMM standalone version missing the Genenetwork2 environment\n")
     pass
 
+progress,info = uses('progress','info')
+
 #np.seterr('raise')
 
 #def run_human(pheno_vector,
@@ -171,10 +173,7 @@ def run_human(pheno_vector,
             #if count > 1000:
             #    break
             count += 1
-
-            percent_complete = (float(count) / total_snps) * 100
-            #print("percent_complete: ", percent_complete)
-            tempdata.store("percent_complete", percent_complete)
+            progress("human",count,total_snps)
 
             #with Bench("actual association"):
             ps, ts = human_association(snp,
@@ -431,10 +430,7 @@ def calculate_kinship_old(genotype_matrix, temp_data=None):
             continue
         keep.append(counter)
         genotype_matrix[:,counter] = (genotype_matrix[:,counter] - values_mean) / np.sqrt(vr)
-        
-        percent_complete = int(round((counter/m)*45))
-        if temp_data != None:
-            temp_data.store("percent_complete", percent_complete)
+        progress('kinship_old',counter,m)
         
     genotype_matrix = genotype_matrix[:,keep]
     print("After kinship (old) genotype_matrix: ", pf(genotype_matrix))
@@ -539,9 +535,8 @@ def GWAS(pheno_vector,
                 lmm_ob.fit(X=x)
             ts, ps, beta, betaVar = lmm_ob.association(x, REML=restricted_max_likelihood)
             
-        percent_complete = 45 + int(round((counter/m)*55))
-        temp_data.store("percent_complete", percent_complete)
-
+        progress("gwas_old",counter,m)
+        
         p_values.append(ps)
         t_statistics.append(ts)
 
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
index e20d4092..b3d480c3 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
@@ -22,7 +22,7 @@ def set_progress_storage(location):
     storage = location
     
 def progress(location, count, total):
-    storage['percentage'] = round(count*100.0)/total)
+    storage.store("percent_complete",round(count*100.0)/total)
     logger.info("Progress: %s %d%%" % (location,round(count*100.0/total)))
 
 def mprint(msg,data):
-- 
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