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):
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( 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 = 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 = log_file
)
self.profile_registry = ProfilesRegistry(self.cfg)
class Test(unittest.TestCase):
_data_dir = os.path.join(os.path.dirname(__file__), "datatest")
def setUp(self):
l = logging.getLogger()
l.manager.loggerDict.clear()
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 = 'NUL' if platform.system() == 'Windows' else '/dev/null'
)
self.profile_registry = ProfilesRegistry(self.cfg)
def tearDown(self):
# close loggers filehandles, so they don't block file deletion
# in shutil.rmtree calls in Windows
logging.shutdown()
l = logging.getLogger()
l.manager.loggerDict.clear()
profile_factory._profiles = {}
try:
shutil.rmtree(self.cfg.working_dir)
except:
pass
def test_get_profile(self):
system_foo = System(self.cfg, "foo", 10)
gene_name = 'sctJ_FLG'
gene = Gene(self.cfg, gene_name, system_foo, self.profile_registry)
profile = profile_factory.get_profile(gene, self.cfg, self.profile_registry )
self.assertTrue( isinstance( profile, Profile ))
self.assertEqual( profile.gene.name, gene_name )
def test_get_uniq_object(self):
system_foo = System(self.cfg, "foo", 10)
gene = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
path = self.profile_registry.get('sctJ_FLG')
profile1 = profile_factory.get_profile(gene, self.cfg, path )
profile2 = profile_factory.get_profile(gene, self.cfg, path)
self.assertEqual( profile1, profile2 )
def test_unknow_profile(self):
system_foo = System(self.cfg, "foo", 10)
gene = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
gene.name = "foo"
self.assertRaises(MacsypyError, profile_factory.get_profile, gene, self.cfg, self.profile_registry)
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'
)
self.profile_registry = ProfilesRegistry(self.cfg)
class Test(unittest.TestCase):
_data_dir = os.path.join(os.path.dirname(__file__), "datatest")
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 tearDown(self):
profile_factory._profiles = {}
shutil.rmtree(self.cfg.working_dir)
def test_get_profile(self):
system_foo = System(self.cfg, "foo", 10)
gene_name = 'sctJ_FLG'
gene = Gene(self.cfg, gene_name, system_foo, self.profile_registry)
profile = profile_factory.get_profile(gene, self.cfg, self.profile_registry )
self.assertTrue( isinstance( profile, Profile ))
self.assertEqual( profile.gene.name, gene_name )
def test_get_uniq_object(self):
system_foo = System(self.cfg, "foo", 10)
gene = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
path = self.profile_registry.get('sctJ_FLG')
profile1 = profile_factory.get_profile(gene, self.cfg, path )
profile2 = profile_factory.get_profile(gene, self.cfg, path)
self.assertEqual( profile1, profile2 )
def test_unknow_profile(self):
system_foo = System(self.cfg, "foo", 10)
gene = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
gene.name = "foo"
self.assertRaises(MacsypyError, profile_factory.get_profile, gene, self.cfg, self.profile_registry)
def setUp(self):
l = logging.getLogger()
l.manager.loggerDict.clear()
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 = 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'
)
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()
class Test(unittest.TestCase):
_data_dir = os.path.join(os.path.dirname(__file__), "datatest")
def setUp(self):
l = logging.getLogger()
l.manager.loggerDict.clear()
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 = 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'
)
self.profile_registry = ProfilesRegistry(self.cfg)
def tearDown(self):
# close loggers filehandles, so they don't block file deletion
# in shutil.rmtree calls in Windows
logging.shutdown
l = logging.getLogger()
l.manager.loggerDict.clear()
try:
shutil.rmtree(self.cfg.working_dir)
except:
pass
def test_len(self):
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
self.assertEqual(len(profile), 501)
def test_str(self):
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
s = "%s : %s" % (gene.name, path)
self.assertEqual(str(profile), s)
@unittest.skipIf( not which('hmmsearch'), 'hmmsearch not found in PATH')
def test_execute(self):
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
report = profile.execute()
hmmer_raw_out = profile.hmm_raw_output
with open(hmmer_raw_out, 'r') as hmmer_raw_out_file:
first_l = hmmer_raw_out_file.readline()
#a hmmsearch output file has been produced
self.assertTrue(first_l.startswith("# hmmsearch :: search profile(s) against a sequence database"))
for i in range(5):
#skip 4 lines
l = hmmer_raw_out_file.readline()
#a hmmsearch used the abc profile line should become with: "# query HMM file:"
path = os.path.join(self.cfg.profile_dir, gene.name + self.cfg.profile_suffix)
self.assertTrue(l.find(path) != -1)
def test_execute_unknown_binary(self):
self.cfg.options['hmmer_exe'] = "Nimportnaoik"
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
self.assertRaises(RuntimeError, profile.execute)
class Test(unittest.TestCase):
_data_dir = os.path.join(os.path.dirname(__file__), "datatest")
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 tearDown(self):
# close loggers filehandles, so they don't block file deletion
# in shutil.rmtree calls in Windows
logging.shutdown()
l = logging.getLogger()
l.manager.loggerDict.clear()
profile_factory._profiles = {}
try:
shutil.rmtree(self.cfg.working_dir)
except:
pass
def test_get_profile(self):
system_foo = System(self.cfg, "foo", 10)
gene_name = 'sctJ_FLG'
gene = Gene(self.cfg, gene_name, system_foo, self.profile_registry)
profile = profile_factory.get_profile(gene, self.cfg,
self.profile_registry)
self.assertTrue(isinstance(profile, Profile))
self.assertEqual(profile.gene.name, gene_name)
def test_get_uniq_object(self):
system_foo = System(self.cfg, "foo", 10)
gene = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
path = self.profile_registry.get('sctJ_FLG')
profile1 = profile_factory.get_profile(gene, self.cfg, path)
profile2 = profile_factory.get_profile(gene, self.cfg, path)
self.assertEqual(profile1, profile2)
def test_unknow_profile(self):
system_foo = System(self.cfg, "foo", 10)
gene = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
gene.name = "foo"
self.assertRaises(MacsypyError, profile_factory.get_profile, gene,
self.cfg, self.profile_registry)
class Test(unittest.TestCase):
_data_dir = os.path.join(os.path.dirname(__file__), "datatest")
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(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=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=log_file)
self.profile_registry = ProfilesRegistry(self.cfg)
def tearDown(self):
# close loggers filehandles, so they don't block file deletion
# in shutil.rmtree calls in Windows
logging.shutdown
l = logging.getLogger()
l.manager.loggerDict.clear()
try:
shutil.rmtree(self.cfg.working_dir)
except:
pass
def test_len(self):
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
self.assertEqual(len(profile), 501)
def test_str(self):
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
s = "{0} : {1}".format(gene.name, path)
self.assertEqual(str(profile), s)
@unittest.skipIf(not which('hmmsearch'), 'hmmsearch not found in PATH')
def test_execute(self):
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
report = profile.execute()
hmmer_raw_out = profile.hmm_raw_output
with open(hmmer_raw_out, 'r') as hmmer_raw_out_file:
first_l = hmmer_raw_out_file.readline()
#a hmmsearch output file has been produced
self.assertTrue(
first_l.startswith(
"# hmmsearch :: search profile(s) against a sequence database"
))
for i in range(5):
#skip 4 lines
l = hmmer_raw_out_file.readline()
#a hmmsearch used the abc profile line should become with: "# query HMM file:"
path = os.path.join(self.cfg.profile_dir,
gene.name + self.cfg.profile_suffix)
self.assertTrue(l.find(path) != -1)
def test_execute_unknown_binary(self):
self.cfg.options['hmmer_exe'] = "Nimportnaoik"
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
self.assertRaises(RuntimeError, profile.execute)
class Test(unittest.TestCase):
_data_dir = os.path.join(os.path.dirname(__file__), "datatest")
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')
self.profile_registry = ProfilesRegistry(self.cfg)
def tearDown(self):
shutil.rmtree(self.cfg.working_dir)
def test_len(self):
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
self.assertEqual(len(profile), 501)
def test_str(self):
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
s = "%s : %s" % (gene.name, path)
self.assertEqual(str(profile), s)
@unittest.skipIf(not which('hmmsearch'), 'hmmsearch not found in PATH')
def test_execute(self):
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
report = profile.execute()
hmmer_raw_out = profile.hmm_raw_output
with open(hmmer_raw_out, 'r') as hmmer_raw_out_file:
first_l = hmmer_raw_out_file.readline()
#a hmmsearch output file has been produced
self.assertTrue(
first_l.startswith(
"# hmmsearch :: search profile(s) against a sequence database"
))
for i in range(5):
#skip 4 lines
l = hmmer_raw_out_file.readline()
#a hmmsearch used the abc profile line should become with: "# query HMM file:"
path = os.path.join(self.cfg.profile_dir,
gene.name + self.cfg.profile_suffix)
self.assertTrue(l.find(path) != -1)
def test_execute_unknown_binary(self):
self.cfg.options['hmmer_exe'] = "Nimportnaoik"
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
self.assertRaises(RuntimeError, profile.execute)
