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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/gwas.py70
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/lmm.py10
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/standalone.py31
3 files changed, 52 insertions, 59 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/gwas.py b/wqflask/wqflask/my_pylmm/pyLMM/gwas.py
index b901c0e2..8b344a90 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/gwas.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/gwas.py
@@ -19,7 +19,6 @@
import pdb
import time
-import sys
# from utility import temp_data
import lmm2
@@ -36,12 +35,10 @@ def formatResult(id,beta,betaSD,ts,ps):
return "\t".join([str(x) for x in [id,beta,betaSD,ts,ps]]) + "\n"
def compute_snp(j,n,snp_ids,lmm2,REML,q = None):
- # print("COMPUTE SNP",j,snp_ids,"\n")
result = []
for snp_id in snp_ids:
snp,id = snp_id
x = snp.reshape((n,1)) # all the SNPs
- # print "X=",x
# if refit:
# L.fit(X=snp,REML=REML)
ts,ps,beta,betaVar = lmm2.association(x,REML=REML,returnBeta=True)
@@ -51,32 +48,28 @@ def compute_snp(j,n,snp_ids,lmm2,REML,q = None):
q = compute_snp.q
q.put([j,result])
return j
- # PS.append(ps)
- # TS.append(ts)
- # return len(result)
- # compute.q.put(result)
- # return None
def f_init(q):
compute_snp.q = q
-def gwas(Y,G,K,restricted_max_likelihood=True,refit=False,verbose=True):
+def gwas(Y,G,K,uses,restricted_max_likelihood=True,refit=False,verbose=True):
"""
- Execute a GWAS. The G matrix should be n inds (cols) x m snps (rows)
+ GWAS. The G matrix should be n inds (cols) x m snps (rows)
"""
+ progress,debug,info,mprint = uses('progress','debug','info','mprint')
+
matrix_initialize()
cpu_num = mp.cpu_count()
numThreads = None # for now use all available threads
kfile2 = False
reml = restricted_max_likelihood
- sys.stderr.write(str(G.shape)+"\n")
+ mprint("G",G)
n = G.shape[1] # inds
inds = n
m = G.shape[0] # snps
snps = m
- sys.stderr.write(str(m)+" SNPs\n")
- # print "***** GWAS: G",G.shape,G
+ info("%s SNPs",snps)
assert snps>inds, "snps should be larger than inds (snps=%d,inds=%d)" % (snps,inds)
# CREATE LMM object for association
@@ -85,19 +78,10 @@ def gwas(Y,G,K,restricted_max_likelihood=True,refit=False,verbose=True):
lmm2 = LMM2(Y,K) # ,Kva,Kve,X0,verbose=verbose)
if not refit:
- if verbose: sys.stderr.write("Computing fit for null model\n")
+ info("Computing fit for null model")
lmm2.fit() # follow GN model in run_other
- if verbose: sys.stderr.write("\t heritability=%0.3f, sigma=%0.3f\n" % (lmm2.optH,lmm2.optSigma))
-
- # outFile = "test.out"
- # out = open(outFile,'w')
- out = sys.stderr
-
- def outputResult(id,beta,betaSD,ts,ps):
- out.write(formatResult(id,beta,betaSD,ts,ps))
- def printOutHead(): out.write("\t".join(["SNP_ID","BETA","BETA_SD","F_STAT","P_VALUE"]) + "\n")
-
- # printOutHead()
+ info("heritability=%0.3f, sigma=%0.3f" % (lmm2.optH,lmm2.optSigma))
+
res = []
# Set up the pool
@@ -106,26 +90,24 @@ def gwas(Y,G,K,restricted_max_likelihood=True,refit=False,verbose=True):
p = mp.Pool(numThreads, f_init, [q])
collect = []
- # Buffers for pvalues and t-stats
- # PS = []
- # TS = []
count = 0
job = 0
jobs_running = 0
+ jobs_completed = 0
for snp in G:
snp_id = (snp,'SNPID')
count += 1
if count % 1000 == 0:
job += 1
- if verbose:
- sys.stderr.write("Job %d At SNP %d\n" % (job,count))
+ debug("Job %d At SNP %d" % (job,count))
if numThreads == 1:
- print "Running on 1 THREAD"
+ debug("Running on 1 THREAD")
compute_snp(job,n,collect,lmm2,reml,q)
collect = []
j,lst = q.get()
- if verbose:
- sys.stderr.write("Job "+str(j)+" finished\n")
+ debug("Job "+str(j)+" finished")
+ jobs_completed += 1
+ progress("GWAS2",jobs_completed,snps/1000)
res.append((j,lst))
else:
p.apply_async(compute_snp,(job,n,collect,lmm2,reml))
@@ -134,8 +116,9 @@ def gwas(Y,G,K,restricted_max_likelihood=True,refit=False,verbose=True):
while jobs_running > cpu_num:
try:
j,lst = q.get_nowait()
- if verbose:
- sys.stderr.write("Job "+str(j)+" finished\n")
+ debug("Job "+str(j)+" finished")
+ jobs_completed += 1
+ progress("GWAS2",jobs_completed,snps/1000)
res.append((j,lst))
jobs_running -= 1
except Queue.Empty:
@@ -150,24 +133,23 @@ def gwas(Y,G,K,restricted_max_likelihood=True,refit=False,verbose=True):
if numThreads==1 or count<1000 or len(collect)>0:
job += 1
- print "Collect final batch size %i job %i @%i: " % (len(collect), job, count)
+ debug("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((j,lst))
- print "count=",count," running=",jobs_running," collect=",len(collect)
+ debug("count=%i running=%i collect=%i" % (count,jobs_running,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")
+ debug("Job "+str(j)+" finished")
+ jobs_completed += 1
+ progress("GWAS2",jobs_completed,snps/1000)
res.append((j,lst))
- print "Before sort",[res1[0] for res1 in res]
+ mprint("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]
+ mprint("After sort",[res1[0] for res1 in res])
+ info([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
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index eab7d91d..1e00002a 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -57,11 +57,11 @@ import gwas
# ---- A trick to decide on the environment:
try:
from wqflask.my_pylmm.pyLMM import chunks
- from gn2 import uses, set_progress_storage
+ from gn2 import uses, progress_set_func
except ImportError:
has_gn2=False
import standalone as handlers
- from standalone import uses, set_progress_storage
+ from standalone import uses, progress_set_func
sys.stderr.write("WARNING: LMM standalone version missing the Genenetwork2 environment\n")
pass
@@ -348,6 +348,7 @@ def run_other_new(pheno_vector,
t_stats, p_values = gwas.gwas(Y,
G.T,
K,
+ uses,
restricted_max_likelihood=True,
refit=False,verbose=True)
Bench().report()
@@ -812,7 +813,10 @@ def gn2_redis(key,species,new_code=True):
params = json.loads(json_params)
tempdata = temp_data.TempData(params['temp_uuid'])
- set_progress_storage(tempdata)
+ def update_tempdata(loc,i,total):
+ tempdata.store("percent_complete",round(i*100.0/total))
+ debug("Updating REDIS percent_complete=%d" % (round(i*100.0/total)))
+ progress_set_func(update_tempdata)
print('kinship', np.array(params['kinship_matrix']))
print('pheno', np.array(params['pheno_vector']))
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
index 7cc3e871..36bf8fd5 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/standalone.py
@@ -17,24 +17,31 @@ logger = logging.getLogger('lmm2')
logging.basicConfig(level=logging.DEBUG)
np.set_printoptions(precision=3,suppress=True)
-last_location = None
-last_progress = 0
+progress_location = None
+progress_current = None
+progress_prev_perc = None
-def set_progress_storage(location):
- global storage
- storage = location
+def progress_default_func(location,count,total):
+ global progress_current
+ value = round(count*100.0/total)
+ progress_current = value
+
+progress_func = progress_default_func
+
+def progress_set_func(func):
+ global progress_func
+ progress_func = func
def progress(location, count, total):
- global last_location
- global last_progress
+ global progress_location
+ global progress_prev_perc
perc = round(count*100.0/total)
- # print(last_progress,";",perc)
- if perc != last_progress and (location != last_location or perc > 98 or perc > last_progress + 5):
- storage.store("percent_complete",perc)
+ if perc != progress_prev_perc and (location != progress_location or perc > 98 or perc > progress_prev_perc + 5):
+ progress_func(location, count, total)
logger.info("Progress: %s %d%%" % (location,perc))
- last_location = location
- last_progress = perc
+ progress_location = location
+ progress_prev_perc = perc
def mprint(msg,data):
"""
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-28 10:31:09 +0000