dest_dir = args.dest
fetch_wgs = args.wgs
extract_wgs = args.extract_wgs
expanded = args.expanded
fetch_meta = args.meta
fetch_index = args.index
aspera = args.aspera
aspera_settings = args.aspera_settings
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)
if __name__ == '__main__':
parser = set_parser()
args = parser.parse_args()
accession = args.accession
format = args.format
dest_dir = args.dest
fetch_wgs = args.wgs
fetch_meta = args.meta
fetch_index = args.index
aspera = args.aspera
try:
if utils.is_wgs_set(accession):
if format is not None:
sequenceGet.check_format(format)
sequenceGet.download_wgs(dest_dir, accession, format)
elif not utils.is_available(accession):
print(
'Record does not exist or is not available for accession provided'
)
sys.exit(1)
elif utils.is_sequence(accession):
if format is not None:
sequenceGet.check_format(format)
sequenceGet.download_sequence(dest_dir, accession, format)
elif utils.is_analysis(accession):
if format is not None:
readGet.check_read_format(format)
readGet.download_files(accession, format, dest_dir, fetch_index,
fetch_meta, aspera)