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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/gn2.py7
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py17
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/standalone.py2
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):