def newZslv(options, zslv_type, tohash=None):
zslv_file = getBasename(os.path.basename(options.dbname)) + getFileSuffix(options, zslv_type, tohash) + ".zslv"
#print "Saving to file:%s" % zslv_file
#return zshelve.open("%s/%s" % (options.output_path, zslv_file))
if "DB" in zslv_type:
zslv_path = os.path.abspath(os.path.dirname(__file__))
return zshelve.open("%s/cache/%s" % (zslv_path, zslv_file))
else:
return zshelve.open("%s/%s" % (options.output_path, zslv_file))
def scanMotifsParallel(options, united, meme_slv, meme_ids):
log = zshelve.open(options.dbname + ".log")
total_num = len(meme_ids) / 100.0
qResults = Queue()
jobs = []
for i, meme_id in enumerate(meme_ids):
fimo = newFIMO(options, meme_slv, [meme_id])
jobs.append(options.parallel.submit(fimo.run, (), (), ('subprocess',)))
for i, (meme_id, job) in enumerate(zip(meme_ids, jobs)):
if meme_id in log.keys():
sys.stderr.write("Skipping:%d%%\t%s\r" % (i / total_num, meme_id))
continue
sys.stderr.write("Scanning:%d%%\t%s\r" % (i / total_num, meme_id))
result = job()
qResults.put((meme_id, result))
while qResults.qsize() > 0:
(meme_id, result) = qResults.get()
united.importScan(result)
log[str(meme_id)] = result
time.sleep(0.5)
folder = md5(str([meme_id])).hexdigest()[:6]
shutil.rmtree(options.output_path + "/%s/" % folder)
shutil.rmtree(options.output_path)
return
def loadZslv(options, zslv_type, tohash=None):
zslv_file = getBasename(os.path.basename(options.dbname)) + getFileSuffix(options, zslv_type, tohash) + ".zslv"
abs_zslv_file = "%s/%s" % (options.output_path, zslv_file)
if os.path.exists(abs_zslv_file):
return zshelve.open("%s/%s" % (options.output_path, zslv_file))
else:
print "%s not exists, run Stats.py first" % abs_zslv_file
sys.exit(1)
def scanMotifs(options, united, meme_slv, meme_ids):
log = zshelve.open(options.dbname + ".log")
total_num = len(meme_ids) / 100.0
for i, meme_id in enumerate(meme_ids):
if meme_id in log.keys():
sys.stderr.write("Skipping:%d%%\t%d\t%s\r" % (i / total_num, len(log.keys()), meme_id))
continue
sys.stderr.write("Scanning:%d%%\t%d\t%s\r" % (i / total_num, len(log.keys()), meme_id))
fimo = newFIMO(options, meme_slv, [meme_id])
result = fimo.run()
united.importScan(result)
log[str(meme_id)] = result
return