def mem_test(num):
for _n in xrange(num):
t0 = time()
c = WorkCounter()
searcher = SearchEngine(abort_event)
results = searcher.find(c, template, primer, 6)
t1 = (time()-t0)
# print 'results use: %fMb' % (asizeof(results)/1024.0/1024.0)
print results
# print_out(results, '')
print '[%6.2f%%] elapsed %f seconds\n' % (c.percent(), t1)
def mem_test(num):
for _n in xrange(num):
t0 = time()
c = WorkCounter()
searcher = SearchEngine(abort_event)
results = searcher.find(c, template, primer, 6)
t1 = (time() - t0)
# print 'results use: %fMb' % (asizeof(results)/1024.0/1024.0)
print results
# print_out(results, '')
print '[%6.2f%%] elapsed %f seconds\n' % (c.percent(), t1)
def find_vs_regexp(primer, template):
find_times = []
re_times = []
for _i in xrange(10):
#find
t0 = time()
searcher = SearchEngine(abort_event)
p_len,t_len = len(primer),len(template)
res = searcher._find(WorkCounter(), template, primer, t_len, p_len, 10)
find_times.append(time()-t0)
#regexp
t0 = time()
fwd_seq = str(template.seq)
rev_seq = str(template.seq.reverse_complement())
primer_re = primer2re(primer)
fwd_res = primer_re.findall(fwd_seq)
rev_res = primer_re.findall(rev_seq)
re_times.append(time()-t0)
print 'find results: f %d, r %d' % (len(res[5]), len(res[6]))
print 're results: f %d, r %d' % (len(fwd_res), len(rev_res))
# print template.seq[res[5][0]:res[5][0]+p_len]
# print fwd_res[0]
return find_times, re_times
def find_vs_regexp(primer, template):
find_times = []
re_times = []
for _i in xrange(10):
#find
t0 = time()
searcher = SearchEngine(abort_event)
p_len, t_len = len(primer), len(template)
res = searcher._find(WorkCounter(), template, primer, t_len, p_len,
10)
find_times.append(time() - t0)
#regexp
t0 = time()
fwd_seq = str(template.seq)
rev_seq = str(template.seq.reverse_complement())
primer_re = primer2re(primer)
fwd_res = primer_re.findall(fwd_seq)
rev_res = primer_re.findall(rev_seq)
re_times.append(time() - t0)
print 'find results: f %d, r %d' % (len(res[5]), len(res[6]))
print 're results: f %d, r %d' % (len(fwd_res), len(rev_res))
# print template.seq[res[5][0]:res[5][0]+p_len]
# print fwd_res[0]
return find_times, re_times
print res[0]
for dup, _id in res[1]:
print _id
print dup
#print 'mismatches:', dup.mismatches
print '\n'
print '\n'
#end def
ppid = os.getpid()
import DegenPrimer.TD_Functions as tdf
from DegenPrimer.SearchEngine import SearchEngine
from DegenPrimer.WorkCounter import WorkCounter
tdf.PCR_P.PCR_T = 60
searcher = SearchEngine(abort_event)
cProfile.runctx('for x in xrange(10): searcher._find(WorkCounter(), template, primer, len(template), len(primer), 6)',
globals(), locals(), 'SearchEngine._find.profile')
matches = searcher._find_mp(WorkCounter(), template[:2000], primer, len(template), len(primer), 6)
cProfile.runctx('for x in xrange(10): searcher.compile_duplexes(WorkCounter(), *matches)',
globals(), locals(), 'SearchEngine.compile_duplexes.profile')
f = 'test_search_results.txt'
dups = searcher.compile_duplexes(WorkCounter(), *matches)
if not os.path.isfile(f):
with open(f, 'w') as out:
out.write(str(dups))
sys.exit()
else:
for dup, _id in res[1]:
print _id
print dup
#print 'mismatches:', dup.mismatches
print '\n'
print '\n'
#end def
ppid = os.getpid()
import DegenPrimer.TD_Functions as tdf
from DegenPrimer.SearchEngine import SearchEngine
from DegenPrimer.WorkCounter import WorkCounter
tdf.PCR_P.PCR_T = 60
searcher = SearchEngine(abort_event)
cProfile.runctx(
'for x in xrange(10): searcher._find(WorkCounter(), template, primer, len(template), len(primer), 6)',
globals(), locals(), 'SearchEngine._find.profile')
matches = searcher._find_mp(WorkCounter(), template[:2000], primer,
len(template), len(primer), 6)
cProfile.runctx(
'for x in xrange(10): searcher.compile_duplexes(WorkCounter(), *matches)',
globals(), locals(), 'SearchEngine.compile_duplexes.profile')
f = 'test_search_results.txt'
dups = searcher.compile_duplexes(WorkCounter(), *matches)
if not os.path.isfile(f):
with open(f, 'w') as out: