def test_build_my_indexes(self):
args = argparse.Namespace()
args.db_type = 'gembase'
args.out_dir = os.path.join(tempfile.gettempdir(),
'test_macsyfinder_indexes')
if os.path.exists(args.out_dir):
shutil.rmtree(
os.path.join(tempfile.gettempdir(),
'test_macsyfinder_indexes'))
os.makedirs(args.out_dir)
seq_db = self.find_data("base", "test_base_with_errors.fa")
shutil.copy(seq_db, args.out_dir)
args.sequence_db = os.path.join(args.out_dir, os.path.basename(seq_db))
self.cfg = Config(MacsyDefaults(), args)
idx = Indexes(self.cfg)
with self.assertRaises(MacsypyError) as e:
# the directory for index exist and is writable but
# the sequence file is corrupted and cannot be read correctly
with self.catch_log():
idx._build_my_indexes(args.out_dir)
self.assertTrue(
str(e.exception).startswith(
"unable to index the sequence dataset:"))
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 setUp(self):
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.res_search_dir = tempfile.gettempdir()
args.log_level = 30
args.out_dir = os.path.join(args.res_search_dir,
'test_macsyfinder_Report')
if os.path.exists(args.out_dir):
shutil.rmtree(args.out_dir)
os.mkdir(args.out_dir)
seq_db = self.find_data("base", "test_base.fa")
shutil.copy(seq_db, args.out_dir)
args.sequence_db = os.path.join(args.out_dir, os.path.basename(seq_db))
self.cfg = Config(MacsyDefaults(), args)
os.mkdir(os.path.join(self.cfg.out_dir(), self.cfg.hmmer_dir()))
self.model_name = 'foo'
self.model_location = ModelLocation(
path=os.path.join(args.models_dir, self.model_name))
# we need to reset the ProfileFactory
# because it's a like a singleton
# so other tests are influenced by ProfileFactory and it's configuration
# for instance search_genes get profile without hmmer_exe
self.profile_factory = ProfileFactory(self.cfg)
idx = Indexes(self.cfg)
idx.build()
def parse(self) -> List[LightHit]:
"""
parse a hmm output file and extract all hits and do some basic computation (coverage profile)
:return: The list of extracted hits
"""
all_hits = []
idx = Indexes(self.cfg)
macsyfinder_idx = idx.build()
my_db = self._build_my_db(self._hmmer_raw_out)
self._fill_my_db(macsyfinder_idx, my_db)
with open(self._hmmer_raw_out, 'r') as hmm_out:
i_evalue_sel = self.cfg.i_evalue_sel()
coverage_threshold = self.cfg.coverage_profile()
hmm_hits = (x[1] for x in groupby(hmm_out, self._hit_start))
# drop summary
next(hmm_hits)
for hmm_hit in hmm_hits:
hit_id = self._parse_hmm_header(hmm_hit)
seq_lg, position_hit = my_db[hit_id]
replicon_name = self._get_replicon_name(hit_id)
body = next(hmm_hits)
l_hit = self._parse_hmm_body(hit_id, self.gene_profile_lg,
seq_lg, coverage_threshold,
replicon_name, position_hit,
i_evalue_sel, body)
all_hits += l_hit
hits = sorted(all_hits, key=lambda h: -h.score)
return hits
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)
def test_build_no_idx(self):
idx = Indexes(self.cfg)
my_idx = idx.build()
self.assertEqual(
my_idx,
os.path.join(os.path.dirname(self.cfg.sequence_db()),
idx.name + ".idx"))
def setUp(self):
self.tmp_dir = os.path.join(tempfile.gettempdir(),
'test_macsyfinder_search_genes')
if os.path.exists(self.tmp_dir):
shutil.rmtree(self.tmp_dir)
os.mkdir(self.tmp_dir)
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_base.fa")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.log_level = 30
args.out_dir = os.path.join(self.tmp_dir, 'job_1')
args.res_search_dir = args.out_dir
os.mkdir(args.out_dir)
self.cfg = Config(MacsyDefaults(), args)
self.model_name = 'foo'
self.model_location = ModelLocation(
path=os.path.join(args.models_dir, self.model_name))
idx = Indexes(self.cfg)
idx._build_my_indexes()
self.profile_factory = ProfileFactory(self.cfg)
def test_fill_my_db(self):
gene_name = "gspD"
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.log_level = 30
args.sequence_db = self.find_data("base", "test_base.fa")
args.index_dir = self.tmpdir
cfg = Config(MacsyDefaults(), args)
gspD_hmmer_path = self.find_data('hmm', 'gspD.search_hmm.out')
idx = Indexes(cfg)
macsyfinder_idx = idx.build()
hmm_prof = macsyprofile.HmmProfile(gene_name, 596, gspD_hmmer_path,
cfg)
db = hmm_prof._build_my_db(gspD_hmmer_path)
hmm_prof._fill_my_db(macsyfinder_idx, db)
self.assertDictEqual(
db, {
'PSAE001c01_031420': (658, 73),
'PSAE001c01_051090': (714, 75),
'PSAE001c01_018920': (776, 71),
'PSAE001c01_043580': (416, 74),
'PSAE001c01_017350': (600, 70),
'PSAE001c01_013980': (759, 69),
'PSAE001c01_026600': (273, 72),
'NC_xxxxx_xx_056141': (803, 141),
'PSAE001c01_006940': (803, 68)
})
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)
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()
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 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,
)
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()
def test_iter(self):
idx = Indexes(self.cfg)
with self.assertRaises(MacsypyError) as ctx:
next(iter(idx))
self.assertEqual(str(ctx.exception), 'Build index before to use it.')
idx.build()
expected_idx = [('VICH001.B.00001.C001_01359', 200, 1),
('VICH001.B.00001.C001_01360', 484, 2),
('VICH001.B.00001.C001_01361', 406, 3),
('VICH001.B.00001.C001_01390', 326, 4),
('VICH001.B.00001.C001_01391', 54, 5),
('VICH001.B.00001.C001_01392', 206, 6),
('VICH001.B.00001.C001_01393', 477, 7),
('VICH001.B.00001.C001_01394', 126, 8),
('VICH001.B.00001.C001_01395', 405, 9),
('VICH001.B.00001.C001_01396', 572, 10),
('VICH001.B.00001.C001_01397', 721, 11),
('VICH001.B.00001.C001_01398', 467, 12),
('VICH001.B.00001.C001_01399', 720, 13),
('VICH001.B.00001.C001_01400', 559, 14),
('VICH001.B.00001.C001_01401', 153, 15),
('VICH001.B.00001.C001_01402', 4558, 16),
('VICH001.B.00001.C001_01500', 120, 17),
('VICH001.B.00001.C001_01501', 344, 18),
('VICH001.B.00001.C001_01502', 478, 19),
('VICH001.B.00001.C001_01503', 724, 20),
('VICH001.B.00001.C001_01504', 309, 21),
('VICH001.B.00001.C001_01505', 390, 22),
('VICH001.B.00001.C001_01506', 419, 23),
('VICH001.B.00001.C001_01540', 353, 24),
('VICH001.B.00001.C001_01541', 229, 25),
('VICH001.B.00001.C001_01542', 267, 26),
('VICH001.B.00001.C001_01543', 328, 27),
('VICH001.B.00001.C001_01544', 258, 28),
('VICH001.B.00001.C001_01545', 228, 29),
('VICH001.B.00001.C001_01546', 538, 30),
('VICH001.B.00001.C001_01547', 77, 31),
('VICH001.B.00001.C001_01548', 476, 32),
('VICH001.B.00001.C001_01549', 324, 33),
('VICH001.B.00001.C001_01550', 387, 34),
('VICH001.B.00001.C001_01551', 382, 35),
('VICH001.B.00001.C001_01552', 149, 36),
('VICH001.B.00001.C001_01553', 319, 37),
('VICH001.B.00001.C001_01554', 237, 38),
('VICH001.B.00001.C001_01555', 74, 39),
('VICH001.B.00001.C001_01556', 362, 40),
('VICH001.B.00001.C001_01557', 170, 41),
('VICH001.B.00001.C001_01558', 77, 42),
('VICH001.B.00001.C001_01559', 296, 43),
('VICH001.B.00001.C001_01560', 405, 44),
('VICH001.B.00001.C001_01561', 182, 45),
('VICH001.B.00001.C001_01562', 445, 46),
('VICH001.B.00001.C001_01563', 212, 47),
('VICH001.B.00001.C001_01564', 387, 48),
('VICH001.B.00001.C001_01565', 414, 49)]
self.assertListEqual(list(iter(idx)), expected_idx)
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_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(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 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'
)
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.ESCO030p01_genes = [('000010', '886'), ('000020', '291'), ('000030', '656'), ('000040', '500'), ('000050', '407'),
('000060', '144'), ('000070', '183'), ('000080', '121'), ('000090', '199'), ('000100', '325'),
('000110', '425'), ('000120', '171'), ('000130', '277'), ('000140', '133'), ('000150', '108'),
('000160', '295'), ('000170', '273'), ('000180', '367'), ('000190', '573'), ('000200', '343'),
('000210', '295'), ('000220', '108'), ('000230', '117'), ('000240', '153'), ('000250', '479'),
('000260', '706'), ('000270', '998'), ('000280', '171'), ('000290', '108'), ('000300', '295'),
('000310', '165'), ('000320', '243'), ('000330', '295'), ('000340', '108'), ('000350', '1755'),
('000360', '248'), ('000370', '286'), ('000380', '186'), ('000390', '83'), ('000400', '153'),
('000410', '69'), ('000420', '295'), ('000430', '108'), ('000440', '145'), ('000450', '59'),
('000460', '124'), ('000470', '246'), ('000480', '325'), ('000490', '54'), ('000500', '95'),
('000510', '83'), ('000520', '56'), ('000530', '401'), ('000540', '320'), ('000550', '256'),
('000560', '73'), ('000570', '144'), ('000580', '258'), ('000590', '133'), ('000600', '140'),
('000610', '63'), ('000620', '138'), ('000630', '68'), ('000640', '169'), ('000650', '127'),
('000660', '295'), ('000670', '108'), ('000670', '108')]
self.PSAE001c01_genes = [('006940', '803'), ('013980', '759'), ('017350', '600'), ('018920', '776'), ('026600', '273'),
('031420', '658'), ('043580', '416'), ('051090', '714'), ('055870', '449'), ('055880', '447'),
('055890', '588'), ('055900', '292'), ('055910', '262'), ('055920', '166'), ('055930', '288'),
('055940', '194'), ('055950', '567'), ('055960', '188'), ('055970', '247'), ('055980', '252'),
('055990', '455'), ('056000', '450'), ('056010', '260'), ('056020', '246'), ('056030', '70'),
('056040', '133'), ('056050', '284'), ('056060', '585'), ('056070', '435'), ('056080', '342'),
('056090', '252'), ('056100', '122'), ('056110', '213'), ('056120', '400'), ('056130', '134'),
('056140', '138'), ('056150', '397'), ('056160', '298'), ('056170', '186'), ('056180', '445'),
('056190', '414'), ('056200', '132'), ('056210', '674'), ('056220', '319'), ('056230', '394'),
('056240', '207'), ('056250', '401'), ('056260', '611'), ('056270', '257'), ('056280', '169'),
('056290', '454'), ('056300', '141'), ('056310', '458'), ('056320', '286'), ('056330', '514'),
('056340', '178'), ('056350', '156'), ('056360', '85'), ('056370', '289'), ('056380', '126'),
('056390', '290'), ('056400', '262'), ('056410', '214'), ('056420', '630'), ('056430', '127'),
('056440', '455'), ('056440', '455')]
idx = Indexes(self.cfg)
idx._build_my_indexes()
def _fill_my_db(self, macsyfinder_idx: str, db: Dict) -> None:
"""
Fill the dictionary with information on the matched sequences
:param macsyfinder_idx: the path the macsyfinder index corresponding to the dataset
:type macsyfinder_idx: string
:param db: the database containing all sequence id of the hits.
:type db: dict
"""
idx = Indexes(self.cfg)
idx.build()
for seqid, length, rank in idx:
if seqid in db:
db[seqid] = (length, rank)
def test_build_not_writable(self):
# Skip test on Windows, since setting the folder permissions is not affecting files inside
# in Singularity container tess are run as root and this test as non sense
idx = Indexes(self.cfg)
idx_dir = os.path.join(os.path.dirname(self.cfg.sequence_db()))
os.chmod(idx_dir, 0000)
try:
with self.assertRaises(IOError) as ctx:
with self.catch_log():
idx.build()
self.assertRegex(str(ctx.exception),
"cannot build indexes, \(.+/test_macsyfinder_indexes\) is not writable")
finally:
os.chmod(idx_dir, 0o777)
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_not_writable(self):
# Skip test on Windows, since setting the folder permissions is not affecting files inside
# in Singularity container tess are run as root and this test as non sense
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)
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_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_hmmer_indexes_all_files_and_pal(self):
idx = Indexes(self.cfg)
# tester tous les fichiers + pal
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq', '.pal')
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')
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_fill_gembase_min_max_oredered_replicon(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)
with self.assertRaises(MacsypyError) as ctx:
with self.catch_log() as log:
db._fill_gembase_min_max({}, self.cfg.replicon_topology())
self.assertEqual(
str(ctx.exception),
f"Error during sequence-db '{self.args.sequence_db}' parsing. "
f"Are you sure db-type is 'gembase'?")
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)
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)
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_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 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()
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()
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'
)
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()
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_my_indexes(self):
args = argparse.Namespace()
args.db_type = 'gembase'
args.e_value_res = 1
args.i_evalue_sel = 0.5
args.models_dir = self.find_data('models')
args.res_search_suffix = ''
args.log_level = 30
args.out_dir = os.path.join(tempfile.gettempdir(), 'test_macsyfinder_indexes')
if os.path.exists(args.out_dir):
shutil.rmtree(os.path.join(tempfile.gettempdir(), 'test_macsyfinder_indexes'))
os.makedirs(args.out_dir)
seq_db = self.find_data("base", "test_base_with_errors.fa")
shutil.copy(seq_db, args.out_dir)
args.sequence_db = os.path.join(args.out_dir, os.path.basename(seq_db))
cfg = Config(MacsyDefaults(), args)
idx = Indexes(cfg)
with self.assertRaises(MacsypyError) as e:
with self.catch_log():
idx._build_my_indexes()
self.assertTrue(str(e.exception).startswith("unable to index the sequence dataset:"))
def test_fill_my_db(self):
gene_name = "gspD"
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
report_path = os.path.join(self.cfg.working_dir(),
gene_name + self.cfg.res_search_suffix())
report = GembaseHMMReport(c_gene, report_path, self.cfg)
idx = Indexes(self.cfg)
macsyfinder_idx = idx.find_my_indexes()
gspD_hmmer_path = self.find_data(
os.path.join('hmm', 'gspD.search_hmm.out'))
db = report._build_my_db(gspD_hmmer_path)
report._fill_my_db(macsyfinder_idx, db)
self.assertDictEqual(
db, {
'PSAE001c01_031420': (658, 73),
'PSAE001c01_051090': (714, 75),
'PSAE001c01_018920': (776, 71),
'PSAE001c01_043580': (416, 74),
'PSAE001c01_017350': (600, 70),
'PSAE001c01_013980': (759, 69),
'PSAE001c01_026600': (273, 72),
'NC_xxxxx_xx_056141': (803, 141),
'PSAE001c01_006940': (803, 68)
})
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_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)
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 fake_init(obj, cfg):
obj.cfg = cfg
idx = Indexes(self.cfg)
obj.sequence_idx = idx.find_my_indexes()
obj.topology_file = self.cfg.topology_file
obj._DB = {}
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 fake_init(obj, cfg):
obj.cfg = cfg
idx = Indexes(self.cfg)
obj.sequence_idx = idx.find_my_indexes()
obj.topology_file = self.cfg.topology_file
obj._DB = {}
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.ESCO030p01_genes = [('000010', '886'), ('000020', '291'),
('000030', '656'), ('000040', '500'),
('000050', '407'), ('000060', '144'),
('000070', '183'), ('000080', '121'),
('000090', '199'), ('000100', '325'),
('000110', '425'), ('000120', '171'),
('000130', '277'), ('000140', '133'),
('000150', '108'), ('000160', '295'),
('000170', '273'), ('000180', '367'),
('000190', '573'), ('000200', '343'),
('000210', '295'), ('000220', '108'),
('000230', '117'), ('000240', '153'),
('000250', '479'), ('000260', '706'),
('000270', '998'), ('000280', '171'),
('000290', '108'), ('000300', '295'),
('000310', '165'), ('000320', '243'),
('000330', '295'), ('000340', '108'),
('000350', '1755'), ('000360', '248'),
('000370', '286'), ('000380', '186'),
('000390', '83'), ('000400', '153'),
('000410', '69'), ('000420', '295'),
('000430', '108'), ('000440', '145'),
('000450', '59'), ('000460', '124'),
('000470', '246'), ('000480', '325'),
('000490', '54'), ('000500', '95'),
('000510', '83'), ('000520', '56'),
('000530', '401'), ('000540', '320'),
('000550', '256'), ('000560', '73'),
('000570', '144'), ('000580', '258'),
('000590', '133'), ('000600', '140'),
('000610', '63'), ('000620', '138'),
('000630', '68'), ('000640', '169'),
('000650', '127'), ('000660', '295'),
('000670', '108'), ('000670', '108')]
self.PSAE001c01_genes = [('006940', '803'), ('013980', '759'),
('017350', '600'), ('018920', '776'),
('026600', '273'), ('031420', '658'),
('043580', '416'), ('051090', '714'),
('055870', '449'), ('055880', '447'),
('055890', '588'), ('055900', '292'),
('055910', '262'), ('055920', '166'),
('055930', '288'), ('055940', '194'),
('055950', '567'), ('055960', '188'),
('055970', '247'), ('055980', '252'),
('055990', '455'), ('056000', '450'),
('056010', '260'), ('056020', '246'),
('056030', '70'), ('056040', '133'),
('056050', '284'), ('056060', '585'),
('056070', '435'), ('056080', '342'),
('056090', '252'), ('056100', '122'),
('056110', '213'), ('056120', '400'),
('056130', '134'), ('056140', '138'),
('056150', '397'), ('056160', '298'),
('056170', '186'), ('056180', '445'),
('056190', '414'), ('056200', '132'),
('056210', '674'), ('056220', '319'),
('056230', '394'), ('056240', '207'),
('056250', '401'), ('056260', '611'),
('056270', '257'), ('056280', '169'),
('056290', '454'), ('056300', '141'),
('056310', '458'), ('056320', '286'),
('056330', '514'), ('056340', '178'),
('056350', '156'), ('056360', '85'),
('056370', '289'), ('056380', '126'),
('056390', '290'), ('056400', '262'),
('056410', '214'), ('056420', '630'),
('056430', '127'), ('056440', '455'),
('056440', '455')]
idx = Indexes(self.cfg)
idx._build_my_indexes()
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)