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()