def proceed_data(self): if not self.running: self.running = True self.trns = trns(self.config_data['input_dir'],self.config_data['output_dir'],self.config_data['output_xml'],self.config_data['log_file'],self.config_data['refresh'],False) self.trns.gui_handler(self) self.trns.start()
import getopt
# default regex
argv = sys.argv
args = arg_parse(argv[1:])
os.chdir(args["in_dir"])
if(args['exprs'] == ''):
exprs = "(?:C[A-Z][A-Z]C[A-Z]{5})([A-Z]{7})(?:H[A-Z]{3}[HC])"
else:
exprs = str(args['exprs'])
parsed = []
if(args["file_type"] == 'fasta'):
for file in glob.glob("*.fas"):
parsed.append(fasta_parser(file))
results = trns(parsed, exprs)
print(results)
out_pretty(results, args["out_file"])
else:
print("Fasta file are the only type currently supported")
sys.exit()
