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
