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src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/bwa/test_bwa.py   seal(Download)
        for src in "bioseq", "qseq":
          seq_pairs = bioseq_pairs if src == "bioseq" else qseq_pairs
          bwsa = bwa.build_bws_array(seq_pairs, qtype=fmt, src=src)
          for j in 0, 1:
            self.assertTrue(type(bwsa[j]) is bwa.bwa_seq_p_t)
  def build_bws_array_with_trim_qual(self):
    pairs = self.load_pairs_fixture("pairs.txt")
    bws_array = bwa.build_bws_array(pairs, qtype="fastq-illumina", src="qseq", trim_qual=15)
    sequences = [ bws_array[read][i] for i in xrange(5) for read in 0,1 ]
    clipped = map(lambda seq: seq.full_len > seq.clip_len, sequences)
  def build_bws_array_with_trim_qual_zero(self):
    pairs = self.load_pairs_fixture("pairs.txt")
    bws_array = bwa.build_bws_array(pairs, qtype="fastq-illumina", src="qseq", trim_qual=0)
    for read in 0,1:
      for i in xrange(len(pairs)):

src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/bwa/test_bwa_memory.py   seal(Download)
  pairs = [x for x in it.izip(read_flow, mate_flow)]
  print_meminfo("AFTER READING PAIRS")
  bwsa = bwa.build_bws_array(pairs)
  print_meminfo("AFTER BUILDING BWSA")
  bwts = bwa.restore_index(refseq_fname)
  pairs = [x for x in it.izip(read_flow, mate_flow)]
  print_meminfo("AFTER READING PAIRS")
  bwsa = bwa.build_bws_array(pairs)
  print_meminfo("AFTER BUILDING BWSA")
  bwts = bwa.restore_index(refseq_fname)

src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/bwa/try_bwa_pairs.py   seal(Download)
    if seq_pairs_read == 0:
      break
    bwsa = bwa.build_bws_array(pairs)
    bwa.cal_sa_reg_gap(0, bwts, seq_pairs_read, bwsa[0], gopt)
    bwa.cal_sa_reg_gap(0, bwts, seq_pairs_read, bwsa[1], gopt)

src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/bwa/test_seq_list_len.py   seal(Download)
    resident_list.append(resident)
 
    bwsa = bwa.build_bws_array(pairs)
    size, resident = print_meminfo("AFTER BUILDING BWSA")
    size_list.append(size)

src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/bwa/try_itermulti.py   seal(Download)
 
  l = len(pairs)
  bwsa = bwa.build_bws_array(pairs)
 
  bwa_iterator = BWAIterator(refseq_fname, gopt, popt, max_isize,

src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/bwa/try_bwa_iterator.py   seal(Download)
 
    l = len(pairs)
    bwsa = bwa.build_bws_array(pairs)
 
    logger = logging.getLogger("test")