if aspera or aspera_settings is not None:
aspera = utils.set_aspera(aspera_settings)
try:
if utils.is_wgs_set(accession):
if output_format is not None:
sequenceGet.check_format(output_format)
sequenceGet.download_wgs(dest_dir, accession, output_format)
elif not utils.is_available(accession):
sys.stderr.write('ERROR: Record does not exist or is not available for accession provided\n')
sys.exit(1)
elif utils.is_sequence(accession):
if output_format is not None:
sequenceGet.check_format(output_format)
sequenceGet.download_sequence(dest_dir, accession, output_format, expanded)
elif utils.is_analysis(accession):
if output_format is not None:
readGet.check_read_format(output_format)
readGet.download_files(accession, output_format, dest_dir, fetch_index, fetch_meta, aspera)
elif utils.is_run(accession) or utils.is_experiment(accession):
if output_format is not None:
readGet.check_read_format(output_format)
readGet.download_files(accession, output_format, dest_dir, fetch_index, fetch_meta, aspera)
elif utils.is_assembly(accession):
if output_format is not None:
assemblyGet.check_format(output_format)
assemblyGet.download_assembly(dest_dir, accession, output_format, fetch_wgs, extract_wgs, expanded)
else:
sys.stderr.write('ERROR: Invalid accession provided\n')
sys.exit(1)
print 'Completed'
'--version',
action='version',
version='%(prog)s 1.2')
return parser
if __name__ == '__main__':
parser = set_parser()
args = parser.parse_args()
accession = args.accession
dest_dir = args.dest
fetch_meta = args.meta
aspera = args.aspera
if not utils.is_analysis(accession):
print(
'Error: Invalid accession. An analysis accession must be provided')
sys.exit(1)
if not utils.is_available(accession):
print(
'Record does not exist or is not available for accession provided')
sys.exit(1)
try:
readGet.download_files(accession, utils.SUBMITTED_FORMAT, dest_dir,
False, fetch_meta, aspera)
print('Completed')
except Exception:
utils.print_error()
