ncbi_names_table, synonymy_table, authority_file, hacks, hacks_data_location, unresolvable_taxonomy_list, keeplist_taxonomy_list, taxa_mappings_list, tax_log_handle, tax_log_html_handle) # tn = name[0] an = name[1] an_flat = krbionames.flatten_organism_name(an, ' ') record.annotations['organism_old'] = record.annotations['organism'] record.annotations['organism'] = an_flat record.annotations['source'] = an_flat record.description = record.description.replace(record.annotations['organism'], '') record.description = record.description.strip() krcl.show_cursor() ######### krseqsearch.__tax_log_close(tax_log_handle) krseqsearch.__tax_log_html_close(tax_log_html_handle) krbioio.write_sequence_file(records, output_file, 'gb')
parser.add_argument('-i', '--input_file', type=unicode, help='Records to download, one per line.') parser.add_argument('-o', '--output_file', type=unicode, help='Results output file.') parser.add_argument('-r', '--cutlist_records_file', type=unicode, help='') parser.add_argument('-t', '--cutlist_taxonomy_file', type=unicode, help='') input_file = None output_file = None cutlist_records_file = None cutlist_taxonomy_file = 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.cutlist_records_file: cutlist_records_file = args.cutlist_records_file if args.cutlist_taxonomy_file: cutlist_taxonomy_file = args.cutlist_taxonomy_file if input_file and output_file and (cutlist_records_file or cutlist_taxonomy_file): records = krbioio.read_sequence_file(input_file, 'gb', ret_type='list') filtered = krseqsearch.filter_records(records, cutlist_records_file, cutlist_taxonomy_file) krbioio.write_sequence_file(filtered, output_file, 'gb')