def download_data(group, data_accession, output_format, group_dir, fetch_wgs,
extract_wgs, expanded, fetch_meta, fetch_index, aspera):
if group == utils.WGS:
print 'Fetching ' + data_accession[:6]
sequenceGet.download_wgs(group_dir, data_accession[:6], output_format)
else:
print 'Fetching ' + data_accession
if group == utils.ASSEMBLY:
assemblyGet.download_assembly(group_dir, data_accession,
output_format, fetch_wgs,
extract_wgs, expanded, True)
elif group in [utils.READ, utils.ANALYSIS]:
readGet.download_files(data_accession, output_format, group_dir,
fetch_index, fetch_meta, aspera)
def download_data(group, data_accession, format, group_dir, fetch_wgs, fetch_meta, fetch_index, aspera):
if group == utils.WGS:
print ('Fetching ' + data_accession[:6])
if aspera:
print ('Aspera not supported for WGS data. Using FTP...')
sequenceGet.download_wgs(group_dir, data_accession[:6], format)
else:
print ('Fetching ' + data_accession)
if group == utils.ASSEMBLY:
if aspera:
print ('Aspera not supported for assembly data. Using FTP...')
assemblyGet.download_assembly(group_dir, data_accession, format, fetch_wgs, True)
elif group in [utils.READ, utils.ANALYSIS]:
readGet.download_files(data_accession, format, group_dir, fetch_index, fetch_meta, aspera)
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'
except Exception:
traceback.print_exc()
utils.print_error()
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()
sys.exit(1)
