def download_sequence_group(accession, format, study_dir):
print('Downloading sequences')
update_accs = []
dest_file = os.path.join(study_dir, utils.get_filename(accession + '_sequences', format))
#sequence update
temp_file = os.path.join(study_dir, 'temp.txt')
download_report(utils.SEQUENCE, utils.SEQUENCE_UPDATE_RESULT, accession, temp_file)
f = open(temp_file)
header = True
for line in f:
if header:
header = False
continue
data_accession = line.strip()
update_accs.append(data_accession)
sequenceGet.append_record(dest_file, data_accession, format)
f.close()
os.remove(temp_file)
#sequence release
temp_file = os.path.join(study_dir, 'temp.txt')
download_report(utils.SEQUENCE, utils.SEQUENCE_RELEASE_RESULT, accession, temp_file)
f = open(temp_file)
header = True
for line in f:
if header:
header = False
continue
data_accession = line.strip()
if data_accession not in update_accs:
sequenceGet.append_record(dest_file, data_accession, format)
f.close()
os.remove(temp_file)
def download_sequence_set(accession_list, mol_type, assembly_dir, format,
quiet):
failed_accessions = []
if len(accession_list) > 0:
if not quiet:
print('fetching sequences: ' + mol_type)
target_file = os.path.join(assembly_dir,
utils.get_filename(mol_type, format))
for accession in accession_list:
success = sequenceGet.append_record(target_file, accession, format)
if not success:
failed_accessions.append(accession)
elif not quiet:
print('no sequences: ' + mol_type)
if len(failed_accessions) > 0:
print('Failed to fetch following ' + mol_type + ', format ' + format)
print(failed_accessions.join(','))