Exemplo n.º 1
0
def main(argv):
  try:
    hit_fn = argv[1]
  except IndexError:
    hit_fn = 'hit_pairs.fastq'
  N = 10
  root_name = 'refseq'
  generate_ref(root_name)
  bwts = bwa.restore_index(root_name)
  bnsp, pacseq = bwa.restore_reference(root_name)
  sys.stderr.write(str(bnsp[0]))
  seq_reader = Bio.SeqIO.parse(open(hit_fn), 'fastq-illumina')
  process_sequences(bwts, bnsp, pacseq, seq_reader, N, print_sams)
  u.clean_up_aux_files(root_name)
Exemplo n.º 2
0
 def tearDown(self):
   for fn in [self.refseq_fn, self.read_fn, self.mate_fn]:
     u.clean_up_aux_files(fn)
Exemplo n.º 3
0
 def tearDown(self):
   if not self.opt.no_clean:
     for fn in [self.refseq_fn, self.read_fn, self.mate_fn]:
       u.clean_up_aux_files(fn)