def check_options(options: ConfigType) -> List[str]:
""" Check the requested PFAM database exists """
database_version = options.fullhmmer_pfamdb_version
pfam_dir = os.path.join(options.database_dir, "pfam")
if database_version == "latest":
database_version = pfamdb.find_latest_database_version(options.database_dir)
return pfamdb.check_db(os.path.join(pfam_dir, database_version))
def check_prereqs() -> List[str]:
""" Ensure at least one database exists and is valid """
failure_messages = []
for binary_name in ['hmmscan']:
if not path.locate_executable(binary_name):
failure_messages.append("Failed to locate executable: %r" % binary_name)
data_dir = get_config().database_dir
try:
version = pfamdb.find_latest_database_version(data_dir)
except ValueError as err:
failure_messages.append(str(err))
return failure_messages
data_path = os.path.join(data_dir, "pfam", version)
failure_messages.extend(pfamdb.check_db(data_path))
return failure_messages
