def test_previous_n_sequence_db(self):
self.parsed_args.previous_run = self.find_data(
os.path.join('data_set', 'results'))
self.parsed_args.sequence_db = self.find_data(
os.path.join('base', 'test_1.fasta'))
with self.catch_log() as log:
cfg = Config(self.defaults, self.parsed_args)
catch_msg = log.get_value().strip()
self.assertEqual(cfg.sequence_db(), 'tests/data/base/test_1.fasta')
self.assertEqual(
f"ignore sequence_db '{self.parsed_args.sequence_db}' "
f"use sequence_db from previous_run '{self.parsed_args.previous_run}'.",
catch_msg)
def test_previous_n_sequence_db(self):
self.parsed_args.previous_run = self.find_data(
os.path.join('data_set', 'results_1'))
sequence_db = self.find_data(os.path.join('base', 'test_1.fasta'))
self.parsed_args.sequence_db = sequence_db
with self.catch_log() as log:
cfg = Config(self.defaults, self.parsed_args)
# The config set the parsed_args.sequence_db to None
catch_msg = log.get_value().strip()
self.assertEqual(cfg.sequence_db(),
'tests/data/base/VICH001.B.00001.C001.prt')
self.maxDiff = None
self.assertEqual(
f"ignore sequence_db '{sequence_db}' use sequence_db from previous_run "
f"'{os.path.abspath(cfg.previous_run())}'.", catch_msg)
class Test(MacsyTest):
def setUp(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_1.fasta")
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)
def tearDown(self):
try:
shutil.rmtree(self.cfg.working_dir())
except:
pass
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")
with open(new_idx, 'w'):
pass
self.assertEqual(idx.find_my_indexes(), new_idx)
def test_build_no_idx(self):
idx = Indexes(self.cfg)
idx.build()
my_idx = idx.find_my_indexes()
self.assertEqual(my_idx, os.path.join(os.path.dirname(self.cfg.sequence_db()), idx.name + ".idx"))
def test_build_with_idx(self):
idx = Indexes(self.cfg)
open(os.path.join(os.path.dirname(self.cfg.sequence_db()), idx.name + ".idx"), 'w').close()
idx.build()
my_idx = idx.find_my_indexes()
self.assertEqual(os.path.getsize(my_idx), 0)
def test_build_force(self):
idx = Indexes(self.cfg)
idx.build(force=True)
my_idx = idx.find_my_indexes()
self.assertNotEqual(os.path.getsize(my_idx), 0)
@unittest.skipIf(platform.system() == 'Windows' or os.getuid() == 0, 'Skip test on Windows or if run as root')
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_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:"))
class TestIndex(MacsyTest):
def setUp(self):
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
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_1.fasta")
shutil.copy(seq_db, args.out_dir)
args.index_dir = args.out_dir
args.sequence_db = os.path.join(args.out_dir, os.path.basename(seq_db))
self.cfg = Config(MacsyDefaults(), args)
def tearDown(self):
try:
shutil.rmtree(self.cfg.working_dir())
except:
pass
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")
with open(new_idx, 'w'):
pass
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 test_build_with_idx(self):
idx = Indexes(self.cfg)
# case new style idx
with open(
os.path.join(os.path.dirname(self.cfg.sequence_db()),
idx.name + ".idx"), 'w') as idx_file:
idx_content_new = f"{self.cfg.sequence_db()}\nVICH001.B.00001.C001_01359{idx._field_separator}200{idx._field_separator}1\n"
idx_file.write(idx_content_new)
my_idx = idx.build()
self.assertEqual(os.path.getsize(idx_file.name), len(idx_content_new))
# case old style no path as first line
idx_path = os.path.join(os.path.dirname(self.cfg.sequence_db()),
idx.name + ".idx")
with open(idx_path, 'w') as idx_file:
idx_content_old = "VICH001.B.00001.C001_01359;200;1\n"
idx_file.write(idx_content_old)
with self.catch_log(log_name='macsypy') as log:
_ = idx.build()
log_msg = log.get_value().strip()
self.assertEqual(
log_msg,
f"The '{idx_path}' index file is in old format. Force index building."
)
# case old style bad separator
idx_path = os.path.join(os.path.dirname(self.cfg.sequence_db()),
idx.name + ".idx")
with open(idx_path, 'w') as idx_file:
idx_content_old = f"{self.cfg.sequence_db()}\nVICH001.B.00001.C001_01359;200;1\n"
idx_file.write(idx_content_old)
with self.catch_log(log_name='macsypy') as log:
_ = idx.build()
log_msg = log.get_value().strip()
self.assertEqual(
log_msg,
f"The '{idx_path}' index file is in old format. Force index building."
)
# case idx seems valid read it
with open(
os.path.join(os.path.dirname(self.cfg.sequence_db()),
idx.name + ".idx")) as idx_file_test:
data = idx_file_test.read()
new_content = f"""{self.cfg.sequence_db()}
VICH001.B.00001.C001_01359{idx._field_separator}200{idx._field_separator}1
VICH001.B.00001.C001_01360{idx._field_separator}484{idx._field_separator}2
VICH001.B.00001.C001_01361{idx._field_separator}406{idx._field_separator}3
VICH001.B.00001.C001_01390{idx._field_separator}326{idx._field_separator}4
VICH001.B.00001.C001_01391{idx._field_separator}54{idx._field_separator}5
VICH001.B.00001.C001_01392{idx._field_separator}206{idx._field_separator}6
VICH001.B.00001.C001_01393{idx._field_separator}477{idx._field_separator}7
VICH001.B.00001.C001_01394{idx._field_separator}126{idx._field_separator}8
VICH001.B.00001.C001_01395{idx._field_separator}405{idx._field_separator}9
VICH001.B.00001.C001_01396{idx._field_separator}572{idx._field_separator}10
VICH001.B.00001.C001_01397{idx._field_separator}721{idx._field_separator}11
VICH001.B.00001.C001_01398{idx._field_separator}467{idx._field_separator}12
VICH001.B.00001.C001_01399{idx._field_separator}720{idx._field_separator}13
VICH001.B.00001.C001_01400{idx._field_separator}559{idx._field_separator}14
VICH001.B.00001.C001_01401{idx._field_separator}153{idx._field_separator}15
VICH001.B.00001.C001_01402{idx._field_separator}4558{idx._field_separator}16
VICH001.B.00001.C001_01500{idx._field_separator}120{idx._field_separator}17
VICH001.B.00001.C001_01501{idx._field_separator}344{idx._field_separator}18
VICH001.B.00001.C001_01502{idx._field_separator}478{idx._field_separator}19
VICH001.B.00001.C001_01503{idx._field_separator}724{idx._field_separator}20
VICH001.B.00001.C001_01504{idx._field_separator}309{idx._field_separator}21
VICH001.B.00001.C001_01505{idx._field_separator}390{idx._field_separator}22
VICH001.B.00001.C001_01506{idx._field_separator}419{idx._field_separator}23
VICH001.B.00001.C001_01540{idx._field_separator}353{idx._field_separator}24
VICH001.B.00001.C001_01541{idx._field_separator}229{idx._field_separator}25
VICH001.B.00001.C001_01542{idx._field_separator}267{idx._field_separator}26
VICH001.B.00001.C001_01543{idx._field_separator}328{idx._field_separator}27
VICH001.B.00001.C001_01544{idx._field_separator}258{idx._field_separator}28
VICH001.B.00001.C001_01545{idx._field_separator}228{idx._field_separator}29
VICH001.B.00001.C001_01546{idx._field_separator}538{idx._field_separator}30
VICH001.B.00001.C001_01547{idx._field_separator}77{idx._field_separator}31
VICH001.B.00001.C001_01548{idx._field_separator}476{idx._field_separator}32
VICH001.B.00001.C001_01549{idx._field_separator}324{idx._field_separator}33
VICH001.B.00001.C001_01550{idx._field_separator}387{idx._field_separator}34
VICH001.B.00001.C001_01551{idx._field_separator}382{idx._field_separator}35
VICH001.B.00001.C001_01552{idx._field_separator}149{idx._field_separator}36
VICH001.B.00001.C001_01553{idx._field_separator}319{idx._field_separator}37
VICH001.B.00001.C001_01554{idx._field_separator}237{idx._field_separator}38
VICH001.B.00001.C001_01555{idx._field_separator}74{idx._field_separator}39
VICH001.B.00001.C001_01556{idx._field_separator}362{idx._field_separator}40
VICH001.B.00001.C001_01557{idx._field_separator}170{idx._field_separator}41
VICH001.B.00001.C001_01558{idx._field_separator}77{idx._field_separator}42
VICH001.B.00001.C001_01559{idx._field_separator}296{idx._field_separator}43
VICH001.B.00001.C001_01560{idx._field_separator}405{idx._field_separator}44
VICH001.B.00001.C001_01561{idx._field_separator}182{idx._field_separator}45
VICH001.B.00001.C001_01562{idx._field_separator}445{idx._field_separator}46
VICH001.B.00001.C001_01563{idx._field_separator}212{idx._field_separator}47
VICH001.B.00001.C001_01564{idx._field_separator}387{idx._field_separator}48
VICH001.B.00001.C001_01565{idx._field_separator}414{idx._field_separator}49
"""
self.assertEqual(data, new_content)
def test_build_force(self):
idx = Indexes(self.cfg)
idx.build(force=True)
my_idx = idx.find_my_indexes()
self.assertNotEqual(os.path.getsize(my_idx), 0)
@unittest.skipIf(platform.system() == 'Windows' or os.getuid() == 0,
'Skip test on Windows or if run as root')
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.assertEqual(f"The '{idx_dir}' dir is not writable.",
str(ctx.exception))
finally:
os.chmod(idx_dir, 0o777)
@unittest.skipIf(platform.system() == 'Windows' or os.getuid() == 0,
'Skip test on Windows or if run as root')
def test_index_dir(self):
# case index-dir is not specify sequence-db dir is not writable
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.out_dir = os.path.join(tempfile.gettempdir(),
'test_macsyfinder_indexes')
args.sequence_db = os.path.join(
args.out_dir, os.path.basename(self.cfg.sequence_db()))
cfg = Config(MacsyDefaults(), args)
idx = Indexes(cfg)
index_dir = idx._index_dir(build=False)
expc_idx_dir = os.path.dirname(cfg.sequence_db())
self.assertEqual(index_dir, expc_idx_dir)
try:
os.chmod(index_dir, 0000)
with self.assertRaises(ValueError) as ctx:
_ = idx._index_dir(build=True)
self.assertEqual(
f"The '{index_dir}' dir is not writable. Change rights or specify --index-dir.",
str(ctx.exception))
finally:
os.chmod(index_dir, 0o777)
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.out_dir = os.path.join(tempfile.gettempdir(),
'test_macsyfinder_indexes')
args.index_dir = os.path.join(args.out_dir, 'index_dir')
args.sequence_db = os.path.join(
args.out_dir, os.path.basename(self.cfg.sequence_db()))
cfg = Config(MacsyDefaults(), args)
idx = Indexes(cfg)
# case --index-dir does not exists
with self.assertRaises(ValueError) as ctx:
_ = idx._index_dir(build=False)
self.assertEqual(str(ctx.exception),
f"No such directory: {args.index_dir}")
# case --index-dir is not writable
os.makedirs(args.index_dir)
os.chmod(args.index_dir, 0000)
try:
# but I do not care I only read
index_dir = idx._index_dir(build=False)
self.assertEqual(index_dir, args.index_dir)
# it's important to build indexes
with self.assertRaises(ValueError) as ctx:
_ = idx._index_dir(build=True)
self.assertEqual(str(ctx.exception),
f"The '{index_dir}' dir is not writable.")
finally:
os.chmod(args.index_dir, 0o777)
# case the sequence_db value is just a filename not a path
current_dir = os.getcwd()
try:
os.chdir(args.out_dir)
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.out_dir = os.path.join(tempfile.gettempdir(),
'test_macsyfinder_indexes')
args.sequence_db = os.path.basename(self.cfg.sequence_db())
cfg = Config(MacsyDefaults(), args)
idx = Indexes(cfg)
idx_dir = idx._index_dir(build=True)
self.assertEqual(idx_dir, os.getcwd())
finally:
os.chdir(current_dir)
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_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_index_dir(self):
# case index-dir is not specify sequence-db dir is not writable
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.out_dir = os.path.join(tempfile.gettempdir(),
'test_macsyfinder_indexes')
args.sequence_db = os.path.join(
args.out_dir, os.path.basename(self.cfg.sequence_db()))
cfg = Config(MacsyDefaults(), args)
idx = Indexes(cfg)
index_dir = idx._index_dir(build=False)
expc_idx_dir = os.path.dirname(cfg.sequence_db())
self.assertEqual(index_dir, expc_idx_dir)
try:
os.chmod(index_dir, 0000)
with self.assertRaises(ValueError) as ctx:
_ = idx._index_dir(build=True)
self.assertEqual(
f"The '{index_dir}' dir is not writable. Change rights or specify --index-dir.",
str(ctx.exception))
finally:
os.chmod(index_dir, 0o777)
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.out_dir = os.path.join(tempfile.gettempdir(),
'test_macsyfinder_indexes')
args.index_dir = os.path.join(args.out_dir, 'index_dir')
args.sequence_db = os.path.join(
args.out_dir, os.path.basename(self.cfg.sequence_db()))
cfg = Config(MacsyDefaults(), args)
idx = Indexes(cfg)
# case --index-dir does not exists
with self.assertRaises(ValueError) as ctx:
_ = idx._index_dir(build=False)
self.assertEqual(str(ctx.exception),
f"No such directory: {args.index_dir}")
# case --index-dir is not writable
os.makedirs(args.index_dir)
os.chmod(args.index_dir, 0000)
try:
# but I do not care I only read
index_dir = idx._index_dir(build=False)
self.assertEqual(index_dir, args.index_dir)
# it's important to build indexes
with self.assertRaises(ValueError) as ctx:
_ = idx._index_dir(build=True)
self.assertEqual(str(ctx.exception),
f"The '{index_dir}' dir is not writable.")
finally:
os.chmod(args.index_dir, 0o777)
# case the sequence_db value is just a filename not a path
current_dir = os.getcwd()
try:
os.chdir(args.out_dir)
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.out_dir = os.path.join(tempfile.gettempdir(),
'test_macsyfinder_indexes')
args.sequence_db = os.path.basename(self.cfg.sequence_db())
cfg = Config(MacsyDefaults(), args)
idx = Indexes(cfg)
idx_dir = idx._index_dir(build=True)
self.assertEqual(idx_dir, os.getcwd())
finally:
os.chdir(current_dir)
