def handle_databases(self):
log.start_logging()
print(ui.header('submodule: databases', level=2))
handler = databases.get_handler(self.config_d)
if self.args.quick:
databases.build_quick_pipeline(handler, self.config_d,
self.databases_d)
else:
databases.build_default_pipeline(handler,
self.config_d,
self.databases_d,
with_uniref=self.args.full,
with_nr=self.args.nr)
if self.args.install:
return databases.install(handler)
else:
databases.check_or_fail(handler)
def setup_method(self):
self.logger = logging.getLogger('tests.test_databases.TestDatabases')
class Args(object):
pass
self.args = Args()
self.args.database_dir = databases.default_database_dir(self.logger)
self.args.verbosity = 2
self.args.full = False
self.args.n_threads = 1
self.args.busco_group = 'metazoa'
self.config, self.databases = get_config()
self.config.update(vars(self.args))
self.handler = databases.get_handler(self.config)
databases.build_default_pipeline(self.handler,
self.config,
self.databases,
with_uniref=False)
def handle_annotate(self):
log.start_logging()
print(ui.header('submodule: annotate', level=2))
db_handler = databases.get_handler(self.config_d)
if self.args.quick:
databases.build_quick_pipeline(db_handler, self.config_d,
self.databases_d)
else:
databases.build_default_pipeline(db_handler,
self.config_d,
self.databases_d,
with_uniref=self.args.full,
with_nr=self.args.nr)
if self.config_d['force'] is True:
utd_msg = '*All database tasks up-to-date.*'
ood_msg = '*Some database tasks out-of-date; '\
'FORCE is True, ignoring!'
uptodate, statuses = db_handler.print_statuses(
uptodate_msg=utd_msg, outofdate_msg=ood_msg)
else:
databases.check_or_fail(db_handler)
annotate_handler = annotate.get_handler(self.config_d,
db_handler.files)
if self.args.quick:
build_quick_pipeline(annotate_handler, self.config_d,
db_handler.files)
elif self.args.full:
build_full_pipeline(annotate_handler, self.config_d,
db_handler.files)
elif self.args.nr:
build_nr_pipeline(annotate_handler, self.config_d,
db_handler.files)
else:
build_default_pipeline(annotate_handler, self.config_d,
db_handler.files)
return annotate.run_annotation(annotate_handler)