def test_seed_init(self):
temp = miRmap(seq_mrn="augcaugc", seq_mir="augc")
self.assertIsInstance(temp._seed, seed.mmSeed)
self.assertEqual(temp._seed.target_seq, "AUGCAUGC")
self.assertEqual(temp._seed.mirna_seq, "AUGC")
self.assertEqual(temp._seed.min_target_length, len("AUGC"))
temp_seed_args = {}
temp_seed_args['seed_args'] = {
'target_seq': 'augcaugcaugc', #: Wont be updated
'mirna_seq': 'cgua', #: Wont be updated
'min_target_length': 2 #: Will be updated
}
temp = miRmap(
seq_mrn="augcaugc", seq_mir="augc", **temp_seed_args
)
self.assertNotEqual(temp._seed.target_seq, "AUGCAUGCAUGC")
self.assertNotEqual(temp._seed.mirna_seq, "CGUA")
self.assertEqual(temp._seed.target_seq, "AUGCAUGC")
self.assertEqual(temp._seed.mirna_seq, "AUGC")
self.assertNotEqual(temp._seed.min_target_length, len("AUGC"))
self.assertEqual(temp._seed.min_target_length, 2)
temp_seed_args['seed_args'] = {
'min_target_length': 10 #: Will be updated
}
temp = miRmap(
seq_mrn="augcaugc", seq_mir="augc", **temp_seed_args
)
self.assertNotEqual(temp._seed.min_target_length, len("AUGC"))
self.assertEqual(temp._seed.min_target_length, 10)
def test_warning_raised(self):
warnings.simplefilter("error")
try:
obj = miRmap(seq_mrn="TEST", seq_mir="TEST")
self.assertIsInstance(
getattr(obj, '_thermodynamic'),
thermodynamics.mmThermo
)
except (RuntimeWarning, AttributeError):
warnings.simplefilter("default")
obj = miRmap(seq_mrn="TEST", seq_mir="TEST")
self.assertFalse(getattr(obj, '_thermodynamic', False))
warnings.simplefilter("default")
def test_model_property(self):
temp = miRmap(seq_mrn="augcaugc", seq_mir="augc")
if getattr(temp, '_thermodynamic', False):
seed_def = 'full_seed'
else:
seed_def = 'python_only_seed'
self.assertEqual(temp.model, seed_def)
self.assertEqual(temp.model_select(6),
temp.models.get(seed_def + '6'))
self.assertEqual(temp.model_select(7),
temp.models.get(seed_def + '7'))
self.assertEqual(temp.model_select(8),
temp.models.get(seed_def + '7'))
temp.model = 'full_seed'
self.assertEqual(temp.model, 'full_seed')
self.assertEqual(temp.model_select(6),
temp.models.get('full_seed6'))
self.assertEqual(temp.model_select(7),
temp.models.get('full_seed7'))
self.assertEqual(temp.model_select(8),
temp.models.get('full_seed7'))
with self.assertRaises(ValueError):
temp.model_select(2)
def setUp(self):
seq_target = (
'GCUACAGUUUUUAUUUAGCAUGGGGAUUGCAGAGUGACCAGCAC'
'ACUGGACUCCGAGGUGGUUCAGACAAGACAGAGGGGAGCAGUGG'
'CCAUCAUCCUCCCGCCAGGAGCUUCUUCGUUCCUGCGCAUAUAG'
'ACUGUACAUUAUGAAGAAUACCCAGGAAGACUUUGUGACUGUCA'
'CUUGCUGCUUUUUCUGCGCUUCAGUAACAAGUGUUGGCAAACGA'
'GACUUUCUCCUGGCCCCUGCCUGCUGGAGAUCAGCAUGCCUGUC'
'CUUUCAGUCUGAUCCAUCCAUCUCUCUCUUGCCUGAGGGGAAAG'
'AGAGAUGGGCCAGGCAGAGAACAGAACUGGAGGCAGUCCAUCUA'
)
seq_mirna = 'UAGCAGCACGUAAAUAUUGGCG'
ini = {
'seq_mir': seq_mirna,
'seq_mrn': seq_target,
'seed_args': {
'allowed_lengths': [6, 7],
'allowed_gu_wobbles': {6: 0, 7: 0},
'allowed_mismatches': {6: 0, 7: 0},
'take_best': True
},
'tscan_args': {
'with_correction': False
},
'prob_args': {
}
}
self.obj = miRmap(**ini)
self.obj.routine()
def test_score(self):
_mirs = utils.load_fasta('tests/input/hsa-miR-30a-3p.fa')
_mrnas = utils.load_fasta('tests/input/NM_024573.fa')
obj = miRmap(seq_mrn=_mrnas['NM_024573'],
seq_mir=_mirs['hsa-miR-30a-3p'])
obj.routine()
self.assertAlmostEqualList(obj._target_scan.tgs_aus,
[-0.05019, -0.11319], places=4)
self.assertAlmostEqualList(obj._target_scan.tgs_pairing3ps,
[0.00312, 0.05150], places=4)
self.assertAlmostEqualList(obj._target_scan.tgs_positions,
[-0.01526, -0.03190], places=4)
self.assertAlmostEqualList(obj._prob_binomial.prob_binomials,
[0.07013, 0.83698], places=4)
try:
self.assertAlmostEqualList(obj._thermodynamic.dg_duplexs,
[-7.50000, -7.70000], places=4)
self.assertAlmostEqualList(obj._thermodynamic.dg_bindings,
[-8.48000, -8.79000], places=4)
self.assertAlmostEqualList(obj._thermodynamic.dg_opens,
[14.10000, 14.10000], places=4)
except AttributeError:
#: Validate if python-only model is used.
self.assertEqual(obj.model, 'python_only_seed')
def test_evolutionary_features(self):
obj = miRmap(**self.init_args)
try:
expected = {
'cons_bls': 0,
'selec_phylop': 0
}
out = obj.evolutionary_features
self.assertEqual(out, expected)
except ValueError:
pass
def test_probability_features(self):
obj = miRmap(**self.init_args)
try:
expected = {
'prob_binomial': 0.03311825751646191,
'prob_exact': 0.06799
}
out = obj.probability_features
self.assertEqual(out, expected)
except ValueError:
pass
def test_eval_score(self):
temp = miRmap(seq_mrn="TEST_MRN", seq_mir="TEST_MIR")
with self.assertRaises(AttributeError):
temp.scores
with self.assertRaises(AttributeError):
temp._eval_score()
temp.routine()
self.assertIsInstance(temp.scores, list)
args = {
'seq_mrn': self._mrnas['NM_024573'],
'seq_mir': self._mirs['hsa-miR-30a-3p'],
}
obj = miRmap(**args)
obj.routine()
self.assertIsInstance(temp.scores, list)
def test_target_scan_features(self):
obj = miRmap(**self.init_args)
try:
expected = {
'tgs_au': 0.6411404871525753,
'tgs_pairing3p': 1.0,
'tgs_position': 166.0
}
out = obj.target_scan_features
self.assertEqual(out, expected)
except ValueError:
pass
def test_thermodynamic_features(self):
obj = miRmap(**self.init_args)
try:
expected = {
'dg_binding_seed': -10.68,
'dg_binding': -11.95,
'dg_open': 12.46,
'dg_duplex_seed': -10.1,
'dg_duplex': -13.8
}
out = obj.thermodynamic_features
self.assertEqual(out, expected)
except ValueError:
pass
def test_init(self):
with self.assertRaises(TypeError):
#: No Args
miRmap()
miRmap(seq_mir="TEST")
miRmap(seq_mrn="TEST")
temp = miRmap(seq_mrn="TEST_MRN", seq_mir="TEST_MIR")
self.assertIsInstance(temp, miRmap, msg="Instance Ok")
self.assertEqual(temp.seq_mrn, "TEST_MRN", msg="mRNA Ok")
self.assertEqual(temp.seq_mir, "TEST_MIR", msg="miRNA Ok")
default_models = {
'full_seed6': {},
'full_seed7': {},
'python_only_seed6': {},
'python_only_seed7': {}
}
self.assertEqual(temp.models.keys(), default_models.keys())
'GCUCUGGAUGAAUAUGAGGAGCUCAAUGUCUGGCAGGUCAAUGCUUCCCGGACACGGAUC'
'ACUUUUGUCUGAUUCCAGCCUGCUUGCAACCCUGGGGUCCUCUUGUUCCCUGCUGGCCUG'
'CCCCUUGGGAAGGGGCAGUGAUGCCUUUGAGGGGAAGGAGGAGCCCCUCUUUCUCCCAUG'
'CUGCACUUACUCCUUUUGCUAAUAAAAGUGUUUGUAGAUUGUCAUCUUCUAGCCUGGGCC'
'UGACUUCCAUUAAAACAGGGUUUUGUGCGUUUUUU'
)
#hsa-miR-3944-5p
seq_mirna_3944 = 'UGUGCAGCAGGCCAACCGAGA'
#: Change seq. here to test various.
ini = {
'seq_mir': seq_mirna,
'seq_mrn': seq_target,
'seed_args': {
'allowed_lengths': [6, 7],
'allowed_gu_wobbles': {6: 0, 7: 0},
'allowed_mismatches': {6: 0, 7: 0},
'take_best': True
},
'tscan_args': {
'with_correction': False
},
'prob_args': {
}
}
obj = miRmap(**ini)
print(obj.report)