Example #1
0
 def __do_pair_align_and_comparison(self,
                                    log_level=logging.WARNING,
                                    pairing_batch_size=None,
                                    seq_list_len=None,
                                    fastq_subfmt="fastq-sanger"):
     u.build_index(self.refseq_fn)
     #--
     start = time.time()
     bwa_res = u.run_bwa_sampe(self.refseq_fn, self.read_fn, self.mate_fn)
     print 'BWA_SAMPE: %f secs' % (time.time() - start)
     #--
     start = time.time()
     py_res = u.run_bwa_py_sampe(self.refseq_fn, self.read_fn, self.mate_fn,
                                 log_level, pairing_batch_size,
                                 seq_list_len, fastq_subfmt)
     print 'PYBWA_SAMPE: %f secs' % (time.time() - start)
     #--
     self.assertEqual(len(bwa_res), len(py_res))
     for o, n in it.izip(bwa_res, py_res):
         for k in o.keys():
             if k == 'name':
                 nn = n[k].rsplit(
                     "/", 1)[0]  # we are dropping the '/[12]' extension
                 self.assertEqual(o[k], nn)
             elif k == 'aux':
                 self.assertEqual(len(o[k]), len(n[k]))
                 for x, y in it.izip(o[k], n[k]):
                     self.assertEqual(x, y)
             else:
                 self.assertEqual(o[k], n[k])
Example #2
0
 def __do_pair_align_and_comparison(self, log_level=logging.WARNING,
                                    pairing_batch_size=None,
                                    seq_list_len=None,
                                    fastq_subfmt="fastq-sanger"):
   u.build_index(self.refseq_fn)
   #--
   start = time.time()
   bwa_res = u.run_bwa_sampe(self.refseq_fn, self.read_fn, self.mate_fn)
   print 'BWA_SAMPE: %f secs' % (time.time() - start)
   #--
   start = time.time()
   py_res =  u.run_bwa_py_sampe(self.refseq_fn, self.read_fn, self.mate_fn,
                                log_level, pairing_batch_size, seq_list_len,
                                fastq_subfmt)
   print 'PYBWA_SAMPE: %f secs' % (time.time() - start)
   #--
   self.assertEqual(len(bwa_res), len(py_res))
   for o, n in it.izip(bwa_res, py_res):
     for k in o.keys():
       if k == 'name':
         nn = n[k].rsplit("/", 1)[0]  # we are dropping the '/[12]' extension
         self.assertEqual(o[k], nn)
       elif k == 'aux':
         self.assertEqual(len(o[k]), len(n[k]))
         for x,y in it.izip(o[k], n[k]):
           self.assertEqual(x, y)
       else:
         self.assertEqual(o[k],n[k])
Example #3
0
 def __compare_step_by_step(self):
   if not self.opt.no_index:
     u.build_index(self.refseq_fn)
   #--
   bwa_res = u.run_bwa_sampe(self.refseq_fn, self.read_fn, self.mate_fn)
   py_res =  u.run_bwa_py_sampe(self.refseq_fn, self.read_fn, self.mate_fn,
                                log_level=self.opt.log_level,
                                pairing_batch_size=self.opt.pairing_batch_size,
                                seq_list_len=self.opt.seq_list_len,
                                fastq_subfmt=self.opt.fastq_subfmt)
   f = open("errors.dump", 'w')
   error_count = 0
   try:
     self.assertEqual(len(bwa_res), len(py_res))
   except AssertionError:
     error_count += 1
     f.write("Error on result n. %d\n" % i)
     f.write("NUMBER OF RESULT FIELDS: %d, %d\n" % (
       len(bwa_res), len(py_res)))
   for i, (o, n) in enumerate(it.izip(bwa_res, py_res)):
     try:
       for k in o.keys():
         if k == 'name':
           nn = n[k].rsplit("/", 1)[0] # we are dropping the '/[12]' extension
           self.assertEqual(o[k], nn)
         elif k == 'aux':
           self.assertEqual(len(o[k]), len(n[k]))
           for x,y in it.izip(o[k], n[k]):
             self.assertEqual(x, y)
         else:
           self.assertEqual(o[k],n[k])
     except AssertionError:
       error_count += 1
       f.write("Error on result n. %d\n" % i)
       for k in o.keys():
         f.write("%r %r %r %r\n" % (k, o[k], n[k], o[k]==n[k]))
       f.write("\n")
   print "error count: %d" % error_count
   f.close()