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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/gwas.py32
1 files changed, 18 insertions, 14 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/gwas.py b/wqflask/wqflask/my_pylmm/pyLMM/gwas.py
index ce7842f7..b901c0e2 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/gwas.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/gwas.py
@@ -110,13 +110,13 @@ def gwas(Y,G,K,restricted_max_likelihood=True,refit=False,verbose=True):
# PS = []
# TS = []
count = 0
+ job = 0
jobs_running = 0
for snp in G:
snp_id = (snp,'SNPID')
count += 1
- # print count,snp_id
if count % 1000 == 0:
- job = count/1000
+ job += 1
if verbose:
sys.stderr.write("Job %d At SNP %d\n" % (job,count))
if numThreads == 1:
@@ -126,7 +126,7 @@ def gwas(Y,G,K,restricted_max_likelihood=True,refit=False,verbose=True):
j,lst = q.get()
if verbose:
sys.stderr.write("Job "+str(j)+" finished\n")
- res.append(lst)
+ res.append((j,lst))
else:
p.apply_async(compute_snp,(job,n,collect,lmm2,reml))
jobs_running += 1
@@ -136,7 +136,7 @@ def gwas(Y,G,K,restricted_max_likelihood=True,refit=False,verbose=True):
j,lst = q.get_nowait()
if verbose:
sys.stderr.write("Job "+str(j)+" finished\n")
- res.append(lst)
+ res.append((j,lst))
jobs_running -= 1
except Queue.Empty:
time.sleep(0.1)
@@ -149,21 +149,25 @@ def gwas(Y,G,K,restricted_max_likelihood=True,refit=False,verbose=True):
collect.append(snp_id)
if numThreads==1 or count<1000 or len(collect)>0:
- print "Running on 1 THREAD"
- compute_snp(count/1000,n,collect,lmm2,reml,q)
+ job += 1
+ print "Collect final batch size %i job %i @%i: " % (len(collect), job, count)
+ compute_snp(job,n,collect,lmm2,reml,q)
collect = []
j,lst = q.get()
- res.append(lst)
+ res.append((j,lst))
print "count=",count," running=",jobs_running," collect=",len(collect)
for job in range(jobs_running):
j,lst = q.get(True,15) # time out
if verbose:
sys.stderr.write("Job "+str(j)+" finished\n")
- res.append(lst)
-
- if verbose:
- print "res=",res[0][0:10]
- print [len(res1) for res1 in res]
- ts = [item[0] for res1 in res for item in res1]
- ps = [item[1] for res1 in res for item in res1]
+ res.append((j,lst))
+
+ print "Before sort",[res1[0] for res1 in res]
+ res = sorted(res,key=lambda x: x[0])
+ # if verbose:
+ # print "res=",res[0][0:10]
+ print "After sort",[res1[0] for res1 in res]
+ print [len(res1[1]) for res1 in res]
+ ts = [item[0] for j,res1 in res for item in res1]
+ ps = [item[1] for j,res1 in res for item in res1]
return ts,ps