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)
Beispiel #2
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    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)