if args.records: records = args.records if args.output_file: output_file = args.output_file if args.email: email = args.email if args.db: db = args.db if (input_file or records) and output_file and email and db: if records: records = records.split(",") elif input_file: records = krio.read_table_file( handle=None, path=input_file, has_headers=False, headers=None, delimiter=",", quotechar='"', stripchar="", commentchar="#", rettype="set", # dict, list, set ) records = [int(x) for x in records] records = sorted(list(records)) records = [str(x) for x in records] krncbi.download_sequence_records(output_file, records, db, email)
hacks = None hacks_data_location = None if args.hacks: hacks = args.hacks.split(',') if args.hacks_data_location: hacks_data_location = dict() for i, hack in enumerate(hacks): hacks_data_location[hack] = args.hacks_data_location.split(',')[i] ncbi_names_table = None if args.ncbi_names_file: ncbi_names_table = krio.read_table_file( path=args.ncbi_names_file, has_headers=False, headers=('tax_id', 'name_txt', 'unique_name', 'name_class'), delimiter='\t|', quotechar=None, stripchar='"', rettype='dict') synonymy_table = None if args.synonymy_file: synonymy_table = krio.read_table_file( path=args.synonymy_file, has_headers=True, headers=None, delimiter=',') unresolvable_taxonomy_list = None if args.unresolvable_taxonomy_file: unresolvable_taxonomy_list = krio.read_table_file( path=args.unresolvable_taxonomy_file, has_headers=True,
format = None args = parser.parse_args() if args.input_file: input_file = args.input_file if args.output_file: output_file = args.output_file if args.format: format = args.format if args.names: names = krio.read_table_file( path=args.names, has_headers=False, headers=None, delimiter=',', quotechar=None, stripchar='"', rettype='set') if not names: names = args.names.split(',') if args.action: action = args.action if input_file and output_file and format: alignment = AlignIO.read(input_file, format) good_sequences = list()