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()
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)
elif utils.is_run(accession) or utils.is_experiment(accession):
if format is not None:
readGet.check_read_format(format)
readGet.download_files(accession, format, dest_dir, fetch_index,
fetch_meta, aspera)
elif utils.is_assembly(accession):
if format is not None:
assemblyGet.check_format(format)
assemblyGet.download_assembly(dest_dir, accession, format,
fetch_wgs)
else:
print('Error: Invalid accession provided')
sys.exit(1)