def setUp(self): l = logging.getLogger() l.manager.loggerDict.clear() #add only one handler to the macsypy logger from macsypy.gene import _log macsy_log = _log.parent log_file = 'NUL' if platform.system() == 'Windows' else '/dev/null' log_handler = logging.FileHandler(log_file) macsy_log.addHandler(log_handler) self.cfg = Config( sequence_db = os.path.join(self._data_dir, "base", "test_base.fa"), db_type = "gembase", hmmer_exe = "", e_value_res = 1, i_evalue_sel = 0.5, def_dir = os.path.join(self._data_dir, 'DEF'), res_search_dir = tempfile.gettempdir(), res_search_suffix = "", profile_dir = os.path.join(self._data_dir, 'profiles'), profile_suffix = ".hmm", res_extract_suffix = "", log_level = 30, log_file = log_file ) self.profile_registry = ProfilesRegistry(self.cfg)
def setUp(self): self.cfg = Config(sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"), db_type="gembase", hmmer_exe="", e_value_res=1, i_evalue_sel=0.5, def_dir=os.path.join(self._data_dir, 'DEF'), res_search_dir="/tmp", res_search_suffix="", profile_dir=os.path.join(self._data_dir, 'profiles'), profile_suffix=".hmm", res_extract_suffix="", log_level=30, log_file='/dev/null') self.profile_registry = ProfilesRegistry(self.cfg)
def setUp(self): self.cfg = Config(hmmer_exe="hmmsearch", sequence_db=os.path.join(self._data_dir, "base", "test_base.fa"), db_type="gembase", e_value_res=1, i_evalue_sel=0.5, def_dir=os.path.join(self._data_dir, 'DEF'), res_search_dir='/tmp', res_search_suffix=".search_hmm.out", profile_dir=os.path.join(self._data_dir, 'profiles'), profile_suffix=".hmm", res_extract_suffix="", log_level=30, log_file='/dev/null') shutil.copy(self.cfg.sequence_db, self.cfg.working_dir) self.cfg.options['sequence_db'] = os.path.join( self.cfg.working_dir, os.path.basename(self.cfg.sequence_db)) self.profile_registry = ProfilesRegistry(self.cfg) idx = Indexes(self.cfg) idx._build_my_indexes()