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)
def tearDown(self): for fn in [self.refseq_fn, self.read_fn, self.mate_fn]: u.clean_up_aux_files(fn)
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)