def download_assembly(dest_dir, accession, output_format, fetch_wgs, extract_wgs, expanded, quiet=False):
if output_format is None:
output_format = utils.EMBL_FORMAT
assembly_dir = os.path.join(dest_dir, accession)
utils.create_dir(assembly_dir)
# download xml
utils.download_record(assembly_dir, accession, utils.XML_FORMAT)
local_xml = utils.get_destination_file(assembly_dir, accession, utils.XML_FORMAT)
# get wgs and sequence report info
wgs_set, sequence_report = parse_assembly_xml(local_xml)
has_sequence_report = False
# download sequence report
if sequence_report is not None:
has_sequence_report = utils.get_ftp_file(sequence_report, assembly_dir)
# parse sequence report and download sequences
wgs_scaffolds = []
wgs_scaffold_cnt = 0
if has_sequence_report:
wgs_scaffolds = download_sequences(sequence_report.split('/')[-1], assembly_dir, output_format, expanded, quiet)
wgs_scaffold_cnt = len(wgs_scaffolds)
if wgs_scaffold_cnt > 0:
if not quiet:
print 'Assembly contains {} WGS scaffolds, will fetch WGS set'.format(wgs_scaffold_cnt)
fetch_wgs = True
else:
fetch_wgs = True
# download wgs set if needed
if wgs_set is not None and fetch_wgs:
if not quiet:
print 'fetching wgs set'
sequenceGet.download_wgs(assembly_dir, wgs_set, output_format)
# extract wgs scaffolds from WGS file
if wgs_scaffold_cnt > 0 and extract_wgs:
extract_wgs_scaffolds(assembly_dir, wgs_scaffolds, wgs_set, output_format, quiet)
def download_assembly(dest_dir,
accession,
output_format,
fetch_wgs,
quiet=False):
if output_format is None:
output_format = utils.EMBL_FORMAT
assembly_dir = os.path.join(dest_dir, accession)
utils.create_dir(assembly_dir)
# download xml
utils.download_record(assembly_dir, accession, utils.XML_FORMAT)
local_xml = utils.get_destination_file(assembly_dir, accession,
utils.XML_FORMAT)
# get wgs and sequence report info
wgs_set, sequence_report = parse_assembly_xml(local_xml)
has_sequence_report = False
# download sequence report
if sequence_report is not None:
has_sequence_report = utils.get_ftp_file(sequence_report, assembly_dir)
# download wgs set if needed
if wgs_set is not None and fetch_wgs:
if not quiet:
print 'fetching wgs set'
sequenceGet.download_wgs(assembly_dir, wgs_set, output_format)
# parse sequence report and download sequences
if has_sequence_report:
download_sequences(
sequence_report.split('/')[-1], assembly_dir, output_format, quiet)
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)
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)
readGet.download_files(accession, output_format, dest_dir, fetch_index, fetch_meta, aspera)