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')
