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()