Пример #1
0
 def test_check_or_fail_fail(self, tmpdir):
     config = self.config.copy()
     config['database_dir'] = str(tmpdir)
     
     handler = databases.get_handler(config)
     databases.build_default_pipeline(handler,
                                      config,
                                      self.databases,
                                      with_uniref=False)
     with pytest.raises(SystemExit):
         databases.check_or_fail(handler)
Пример #2
0
    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)
Пример #3
0
    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)
Пример #4
0
    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)