diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/gwas.py | 32 |
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 |