def test_fill_ordered_replicon_min_max(self): self.tearDown() self.cfg = Config( hmmer_exe = "hmmsearch", sequence_db = os.path.join(self._data_dir, "base", "ordered_replicon_base"), db_type = "ordered_replicon", 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 = ".search_hmm.out", profile_dir = os.path.join(self._data_dir, 'profiles'), profile_suffix = ".hmm", res_extract_suffix = "", log_level = 30, log_file = 'NUL' if platform.system() == 'Windows' else '/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)) idx = Indexes(self.cfg) idx._build_my_indexes() RepliconDB.__init__ = self.fake_init db = RepliconDB(self.cfg) db._fill_ordered_min_max(self.cfg.replicon_topology) self.assertEqual(len(db._DB), 1) rep = db[RepliconDB.ordered_replicon_name] self.assertEqual(rep.topology, self.cfg.replicon_topology) self.assertEqual(rep.min, 1) self.assertEqual(rep.max, 52)
def test_fill_ordered_replicon_min_max(self): self.tearDown() self.cfg = Config(hmmer_exe="hmmsearch", sequence_db=os.path.join(self._data_dir, "base", "ordered_replicon_base"), db_type="ordered_replicon", 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)) idx = Indexes(self.cfg) idx._build_my_indexes() RepliconDB.__init__ = self.fake_init db = RepliconDB(self.cfg) db._fill_ordered_min_max(self.cfg.replicon_topology) self.assertEqual(len(db._DB), 1) rep = db[RepliconDB.ordered_replicon_name] self.assertEqual(rep.topology, self.cfg.replicon_topology) self.assertEqual(rep.min, 1) self.assertEqual(rep.max, 52)
def test_fill_ordered_replicon_min_max(self): seq_ori = self.find_data("base", "ordered_replicon_base.fasta") shutil.copy(seq_ori, self.args.out_dir) self.args.sequence_db = os.path.join(self.args.out_dir, os.path.basename(seq_ori)) cfg = Config(MacsyDefaults(), self.args) idx = Indexes(cfg) idx.build() RepliconDB.__init__ = self.fake_init db = RepliconDB(cfg) db._fill_ordered_min_max(cfg.replicon_topology()) self.assertEqual(len(db._DB), 1) rep = db[RepliconDB.ordered_replicon_name] self.assertEqual(rep.topology, cfg.replicon_topology()) self.assertEqual(rep.min, 1) self.assertEqual(rep.max, 52)