def test_build_no_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
idx = Indexes(self.cfg)
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
self.assertEqual(my_idx, os.path.join( os.path.dirname(self.cfg.sequence_db), idx.name + ".idx"))
self.assertEqual( hmmer_idx , [ self.cfg.sequence_db + suffix for suffix in ('.phr', '.pin', '.psd', '.psi', '.psq')])
def test_build_no_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
idx = Indexes(self.cfg)
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
self.assertEqual(my_idx, os.path.join( os.path.dirname(self.cfg.sequence_db), idx.name + ".idx"))
self.assertEqual( hmmer_idx , [ self.cfg.sequence_db + suffix for suffix in ('.phr', '.pin', '.psd', '.psi', '.psq')])
def test_build_with_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
#put fake hmmer indexes
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
for s in suffixes:
new_idx = os.path.join( self.cfg.sequence_db + s)
open(new_idx, 'w')
idx = Indexes(self.cfg)
new_idx = open(os.path.join( os.path.dirname(self.cfg.sequence_db), idx.name + ".idx"), 'w')
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
for f in hmmer_idx +[my_idx]:
self.assertEqual(os.path.getsize(f), 0)
def test_build_with_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
#put fake hmmer indexes
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
for s in suffixes:
new_idx = os.path.join( self.cfg.sequence_db + s)
open(new_idx, 'w')
idx = Indexes(self.cfg)
new_idx = open(os.path.join( os.path.dirname(self.cfg.sequence_db), idx.name + ".idx"), 'w')
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
for f in hmmer_idx +[my_idx]:
self.assertEqual(os.path.getsize(f), 0)
class Test(unittest.TestCase):
_data_dir = os.path.join(os.path.dirname(__file__), "datatest")
def __init__(self, methodName='runTest'):
super(Test, self).__init__(methodName)
def fake_init(obj, cfg):
obj.cfg = cfg
obj._fasta_path = cfg.sequence_db
obj.name = os.path.basename(cfg.sequence_db)
self.fake_init = fake_init
self.real_init = Indexes.__init__
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))
def tearDown(self):
try:
shutil.rmtree(self.cfg.working_dir)
except:
pass
def test_find_hmmer_indexes_no_files(self):
idx = Indexes(self.cfg)
#tester pas de fichier
hmmer_idx = idx.find_hmmer_indexes()
self.assertListEqual(hmmer_idx, [])
def test_find_hmmer_indexes_all_files(self):
idx = Indexes(self.cfg)
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
files_2_find = []
for s in suffixes:
new_idx = os.path.join(self.cfg.sequence_db + s)
open(new_idx, 'w')
files_2_find.append(new_idx)
hmmer_idx = idx.find_hmmer_indexes()
self.assertListEqual(hmmer_idx, files_2_find)
def test_find_hmmer_indexes_all_files_and_pal(self):
idx = Indexes(self.cfg)
#tester tous les fichiers + pal
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq', '.pal')
files_2_find = []
for s in suffixes:
new_idx = os.path.join(self.cfg.sequence_db + s)
open(new_idx, 'w')
self.assertRaises(RuntimeError, idx.find_hmmer_indexes)
def test_find_hmmer_indexes_some_files(self):
idx = Indexes(self.cfg)
#tester pas tous les fichiers
suffixes = ('.phr', '.pin', '.psd', '.psi')
files_2_find = []
for s in suffixes:
new_idx = os.path.join(self.cfg.sequence_db + s)
open(new_idx, 'w')
self.assertRaises(RuntimeError, idx.find_hmmer_indexes)
def test_find_hmmer_indexes_lack_pal(self):
idx = Indexes(self.cfg)
#tester plusieurs index pas de pal
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
files_2_find = []
for s in suffixes:
for i in range(2):
new_idx = os.path.join(self.cfg.sequence_db + str(i) + s)
open(new_idx, 'w')
self.assertRaises(RuntimeError, idx.find_hmmer_indexes)
def test_find_hmmer_indexes_all_files_and_2virtual(self):
idx = Indexes(self.cfg)
#tester 1 fichier index + pal
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq', '.pal')
files_2_find = []
for s in suffixes:
for i in range(2):
new_idx = os.path.join(self.cfg.sequence_db + str(i) + s)
open(new_idx, 'w')
files_2_find.append(new_idx)
self.assertRaises(RuntimeError, idx.find_hmmer_indexes)
def test_find_hmmer_indexes_all_files_and_virtual(self):
idx = Indexes(self.cfg)
#tester index + pal
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
files_2_find = []
for s in suffixes:
for i in range(2):
new_idx = os.path.join("%s.%d.%s" %
(self.cfg.sequence_db, i, s))
open(new_idx, 'w')
files_2_find.append(new_idx)
new_idx = os.path.join(self.cfg.sequence_db + '.pal')
open(new_idx, 'w')
files_2_find.append(new_idx)
files_2_find.sort()
hmmer_idx = idx.find_hmmer_indexes()
hmmer_idx.sort()
self.assertListEqual(hmmer_idx, files_2_find)
def test_find_my_indexes(self):
idx = Indexes(self.cfg)
self.assertIsNone(idx.find_my_indexes())
new_idx = os.path.join(os.path.dirname(self.cfg.sequence_db),
idx.name + ".idx")
open(new_idx, 'w')
self.assertEqual(idx.find_my_indexes(), new_idx)
@unittest.skipIf(not (which('makeblastdb') or which('formatdb')),
'neither makeblast nor formatdb found in PATH')
def test_build_no_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
idx = Indexes(self.cfg)
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
self.assertEqual(
my_idx,
os.path.join(os.path.dirname(self.cfg.sequence_db),
idx.name + ".idx"))
self.assertEqual(hmmer_idx, [
self.cfg.sequence_db + suffix
for suffix in ('.phr', '.pin', '.psd', '.psi', '.psq')
])
@unittest.skipIf(not (which('makeblastdb') or which('formatdb')),
'neither makeblast nor formatdb found in PATH')
def test_build_with_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
#put fake hmmer indexes
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
for s in suffixes:
new_idx = os.path.join(self.cfg.sequence_db + s)
open(new_idx, 'w')
idx = Indexes(self.cfg)
new_idx = open(
os.path.join(os.path.dirname(self.cfg.sequence_db),
idx.name + ".idx"), 'w')
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
for f in hmmer_idx + [my_idx]:
self.assertEqual(os.path.getsize(f), 0)
@unittest.skipIf(not (which('makeblastdb') or which('formatdb')),
'neither makeblast nor formatdb found in PATH')
def test_build_force(self):
#put fake hmmer indexes
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
for s in suffixes:
new_idx = os.path.join(self.cfg.sequence_db + s)
open(new_idx, 'w')
idx = Indexes(self.cfg)
new_idx = open(
os.path.join(os.path.dirname(self.cfg.sequence_db),
idx.name + ".idx"), 'w')
idx.build(force=True)
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
for f in hmmer_idx + [my_idx]:
self.assertNotEqual(os.path.getsize(f), 0)
def test_build_not_writable(self):
idx = Indexes(self.cfg)
idx_dir = os.path.join(os.path.dirname(self.cfg.sequence_db))
os.chmod(idx_dir, 0000)
self.assertRaises(IOError, idx.build)
os.chmod(idx_dir, 0777)
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 __init__(self, methodName = 'runTest'):
super(Test, self).__init__(methodName)
def fake_init(obj, cfg):
obj.cfg = cfg
obj._fasta_path = cfg.sequence_db
obj.name = os.path.basename(cfg.sequence_db)
self.fake_init = fake_init
self.real_init = Indexes.__init__
def setUp(self):
l = logging.getLogger()
l.manager.loggerDict.clear()
#add only one handler to the macsypy logger
from macsypy.database 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
)
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))
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_find_hmmer_indexes_no_files(self):
idx = Indexes(self.cfg)
#tester pas de fichier
hmmer_idx = idx.find_hmmer_indexes()
self.assertListEqual(hmmer_idx, [])
def test_find_hmmer_indexes_all_files(self):
idx = Indexes(self.cfg)
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
files_2_find = []
for s in suffixes:
new_idx = os.path.join(self.cfg.sequence_db + s)
open(new_idx, 'w')
files_2_find.append(new_idx)
hmmer_idx = idx.find_hmmer_indexes()
self.assertListEqual(hmmer_idx, files_2_find)
def test_find_hmmer_indexes_all_files_and_pal(self):
idx = Indexes(self.cfg)
#tester tous les fichiers + pal
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq', '.pal')
files_2_find = []
for s in suffixes:
new_idx = os.path.join(self.cfg.sequence_db + s)
open(new_idx, 'w')
self.assertRaises(RuntimeError, idx.find_hmmer_indexes)
def test_find_hmmer_indexes_some_files(self):
idx = Indexes(self.cfg)
#tester pas tous les fichiers
suffixes = ('.phr', '.pin', '.psd', '.psi')
files_2_find = []
for s in suffixes:
new_idx = os.path.join(self.cfg.sequence_db + s)
open(new_idx, 'w')
self.assertRaises(RuntimeError, idx.find_hmmer_indexes)
def test_find_hmmer_indexes_lack_pal(self):
idx = Indexes(self.cfg)
#tester plusieurs index pas de pal
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
files_2_find = []
for s in suffixes:
for i in range(2):
new_idx = os.path.join(self.cfg.sequence_db+ str(i) + s)
open(new_idx, 'w')
self.assertRaises(RuntimeError, idx.find_hmmer_indexes)
def test_find_hmmer_indexes_all_files_and_2virtual(self):
idx = Indexes(self.cfg)
#tester 1 fichier index + pal
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq', '.pal')
files_2_find = []
for s in suffixes:
for i in range(2):
new_idx = os.path.join(self.cfg.sequence_db+ str(i) + s)
open(new_idx, 'w')
files_2_find.append(new_idx)
self.assertRaises(RuntimeError, idx.find_hmmer_indexes)
def test_find_hmmer_indexes_all_files_and_virtual(self):
idx = Indexes(self.cfg)
#tester index + pal
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
files_2_find = []
for s in suffixes:
for i in range(2):
new_idx = os.path.join("{0}.{1:d}.{2}".format(self.cfg.sequence_db, i, s))
open(new_idx, 'w')
files_2_find.append(new_idx)
new_idx = os.path.join(self.cfg.sequence_db + '.pal')
open(new_idx, 'w')
files_2_find.append(new_idx)
files_2_find.sort()
hmmer_idx = idx.find_hmmer_indexes()
hmmer_idx.sort()
self.assertListEqual(hmmer_idx, files_2_find)
def test_find_my_indexes(self):
idx = Indexes(self.cfg)
self.assertIsNone(idx.find_my_indexes())
new_idx = os.path.join(os.path.dirname(self.cfg.sequence_db), idx.name + ".idx")
open(new_idx, 'w')
self.assertEqual(idx.find_my_indexes(), new_idx)
@unittest.skipIf( not (which('makeblastdb') or which('formatdb')) , 'neither makeblast nor formatdb found in PATH')
def test_build_no_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
idx = Indexes(self.cfg)
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
self.assertEqual(my_idx, os.path.join( os.path.dirname(self.cfg.sequence_db), idx.name + ".idx"))
self.assertEqual( hmmer_idx , [ self.cfg.sequence_db + suffix for suffix in ('.phr', '.pin', '.psd', '.psi', '.psq')])
@unittest.skipIf( not (which('makeblastdb') or which('formatdb')) , 'neither makeblast nor formatdb found in PATH')
def test_build_with_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
#put fake hmmer indexes
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
for s in suffixes:
new_idx = os.path.join( self.cfg.sequence_db + s)
open(new_idx, 'w')
idx = Indexes(self.cfg)
new_idx = open(os.path.join( os.path.dirname(self.cfg.sequence_db), idx.name + ".idx"), 'w')
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
for f in hmmer_idx +[my_idx]:
self.assertEqual(os.path.getsize(f), 0)
@unittest.skipIf( not (which('makeblastdb') or which('formatdb')) , 'neither makeblast nor formatdb found in PATH')
def test_build_force(self):
#put fake hmmer indexes
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
for s in suffixes:
new_idx = os.path.join( self.cfg.sequence_db + s)
open(new_idx, 'w')
idx = Indexes(self.cfg)
new_idx = open(os.path.join( os.path.dirname(self.cfg.sequence_db), idx.name + ".idx"), 'w')
idx.build(force = True)
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
for f in hmmer_idx +[my_idx]:
self.assertNotEqual(os.path.getsize(f), 0)
def test_build_not_writable(self):
idx = Indexes(self.cfg)
idx_dir = os.path.join( os.path.dirname(self.cfg.sequence_db))
# Skip test on Windows, since setting the folder permissions is not affecting files inside
if platform.system() != 'Windows':
os.chmod(idx_dir, 0000)
self.assertRaises(IOError, idx.build)
os.chmod(idx_dir, 0777)
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)