def _init_design(self) -> Structure: """ convert into nanodesign structure""" converter = Converter() converter.modify = True converter.read_cadnano_file(self.json, None, self.seq) converter.dna_structure.compute_aux_data() return converter.dna_structure
def read_file(args, logger): """ Read in a cadnano file. """ converter = Converter() logger = logging.getLogger('nanodesign.visualizer') converter.logger = logger if args.infile == None: logger.error("No input file name given.") sys.exit(1) else: logger.info("Input file name: %s" % args.infile) infile = args.infile converter.read_cadnano_file( args.infile, args.inseqfile, args.inseqname ) return converter
def _create_hps_modifications(self) -> Tuple[List, List]: """ create a list of all modified cadnano bases positions.""" # TODO: implement without reusing converter converter = Converter() converter.modify = False converter.read_cadnano_file(self.json, None, self.seq) converter.dna_structure.compute_aux_data() dna_structure_del_ins = converter.dna_structure hps_deletions = list() hps_insertions = list() for strand in dna_structure_del_ins.strands: for base in strand.tour: if base.num_insertions != 0: hps_insertions.append(_hps(base)) elif base.num_deletions != 0: hps_deletions.append(_hps(base)) return hps_deletions, hps_insertions
def read_file(file_name, seq_name): """ Read in a cadnano file. """ converter = Converter() seq_file = None converter.read_cadnano_file(file_name, seq_file, seq_name) return converter
def read_file(file_name, seq_name): # read file converter = Converter() seq_file = None converter.read_cadnano_file(file_name, seq_file, seq_name) return converter