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 write_colored_json(data, dna_structure, colormap, output_file, limits): # write cadnano file colorcoded using a 2D list [[index, value], [index+1, value],...]
if len(limits)>0:
x_min = limits[0]
x_max = limits[1]
else: # if no limits are given, use max and min
x_min = min([data[i][1] for i in range(len(data))])
x_max = max([data[i][1] for i in range(len(data))])
dna_structure_out = dna_structure
for i in range(len(data)):
x = data[i][1]
colorindex = int(254*(x-x_min)/(x_max-x_min))+1 # asumin 0-255 colors in colormap
dna_structure_out.strands[data[i][0]].color = list(colormap(colorindex)[0:-1])
con = Converter()
con.dna_structure = dna_structure_out
con.write_cadnano_file(output_file)
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