def run_basta(self,args):
if args.subparser_name == 'sequence':
self._check_dir(args)
if not dbutils._check_complete(args.directory):
self.logger.error("\n[BASTA ERROR] Couldn't find complete_taxa.db in %s. Did you run initial \'basta download\'?" % (args.directory))
sys.exit()
self._basta_sequence(args)
elif args.subparser_name == 'single':
self._check_dir(args)
if not dbutils._check_complete(args.directory):
self.logger.error("\n[BASTA ERROR] Couldn't find complete_taxa.db in %s. Did you run initial \'basta download\'?" % (args.directory))
sys.exit()
self._basta_single(args)
elif args.subparser_name == 'multiple':
self._check_dir(args)
if not dbutils._check_complete(args.directory):
self.logger.error("\n[BASTA ERROR] Couldn't find complete_taxa.db in %s. Did you run initial \'basta download\'?" % (args.directory))
sys.exit()
self._basta_multiple(args)
elif args.subparser_name == 'download':
self._check_dir(args)
self._basta_download(args)
elif args.subparser_name == 'create_db':
self._check_dir(args)
self._basta_create_db(args)
elif args.subparser_name == 'taxonomy':
self._check_dir(args)
self._basta_taxonomy(args)
def test_check_complete(self):
os.mkdir(os.path.join(self.pwd, "complete_taxa.db"))
self.assertTrue(db._check_complete(self.pwd))
os.rmdir(os.path.join(self.pwd, "complete_taxa.db"))