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)
