def test_init_args(self):
obj = targetscan.mmTargetScan(
seed=self.seed,
with_correction=False)
self.assertEqual(obj.with_correction, False)
self.assertEqual(obj.ca_window_length, 30)
obj = targetscan.mmTargetScan(
seed=self.seed,
with_correction=False,
ca_window_length=10)
self.assertEqual(obj.with_correction, False)
self.assertEqual(obj.ca_window_length, 10)
obj = targetscan.mmTargetScan(
seed=self.seed,
ca_window_length=10)
self.assertEqual(obj.with_correction, True)
self.assertEqual(obj.ca_window_length, 10)
obj = targetscan.mmTargetScan(
seed=self.seed,
unwanted=True,
ca_window_length=20)
self.assertEqual(obj.with_correction, True)
self.assertEqual(obj.ca_window_length, 20)
with self.assertRaises(AttributeError):
obj.unwanted
def test_init(self):
with self.assertRaises(TypeError):
targetscan.mmTargetScan()
obj = targetscan.mmTargetScan(seed=self.seed)
self.assertIsInstance(obj, targetscan.mmTargetScan)
self.assertEqual(obj.seed, self.seed)
def test_init_defaults(self):
obj = targetscan.mmTargetScan(seed=self.seed)
self.assertEqual(obj.with_correction, True)
self.assertEqual(obj.ca_window_length, 30)
self.assertIsInstance(obj.ts_types, dict)
type_key = ['6mer', '7mer-A1', '7mer-m8', '8mer']
types_keys = [
'name',
'up_shift',
'down_shift',
'fc_mean',
'ca_fc_slope',
'ca_fc_intercept',
'ca_weights_up',
'ca_weights_down',
'po_fc_slope',
'po_fc_intercept',
'pa_fc_slope',
'pa_fc_intercept',
'pa_mirna_seed_start',
'pa_mirna_seed_overhang',
]
type_val_tuple = namedtuple('TSTypes', types_keys)
for key in type_key:
self.assertIn(key, obj.ts_types.keys())
for key in obj.ts_types:
self.assertEqual(obj.ts_types[key]._fields,
type_val_tuple._fields)
def test_routine(self):
obj = targetscan.mmTargetScan(seed=self.seed)
with self.assertRaises(AttributeError):
obj.tgs_scores
with self.assertRaises(AttributeError):
obj.tgs_positions
with self.assertRaises(AttributeError):
obj.tgs_pairing3ps
with self.assertRaises(AttributeError):
obj.tgs_scores
obj.routine()
raus = [-0.0501892775521989, -0.11318565255796981]
self.assertAlmostEqualList(obj.tgs_aus, raus)
rpos = [-0.015256000000000002, -0.031904]
self.assertAlmostEqualList(obj.tgs_positions, rpos)
r3ps = [0.003119999999999999, 0.051500000000000004]
self.assertAlmostEqualList(obj.tgs_pairing3ps, r3ps)
rscore = [-0.07732527755219891, -0.2545896525579698]
self.assertAlmostEqualList(obj.tgs_scores, rscore)
def test_eval_tgs_score(self):
obj = targetscan.mmTargetScan(seed=self.seed)
with self.assertRaises(AttributeError):
obj.tgs_scores
with self.assertRaises(AttributeError):
obj._eval_tgs_score()
obj._eval_tgs_au()
with self.assertRaises(AttributeError):
obj._eval_tgs_score()
obj._eval_tgs_position()
with self.assertRaises(AttributeError):
obj._eval_tgs_score()
obj._eval_tgs_pairing3p()
t1 = obj._eval_tgs_score()
r1 = [-0.07732527755219891, -0.2545896525579698]
self.assertAlmostEqualList(t1, r1)
self.assertAlmostEqualList(obj.tgs_scores, r1)
self.assertAlmostEqual(obj.tgs_score, max(r1), places=5)
def test_targetscan_ts_type(self):
obj = targetscan.mmTargetScan(seed=self.seed)
self.assertEqual(obj._targetscan_ts_type(6, 'A'), '8mer')
self.assertEqual(obj._targetscan_ts_type(6, 'T'), '7mer-m8')
self.assertEqual(obj._targetscan_ts_type(7, 'A'), '7mer-A1')
self.assertEqual(obj._targetscan_ts_type(8, 'A'), '7mer-A1')
self.assertEqual(obj._targetscan_ts_type(7, 'T'), '6mer')
with self.assertRaises(ValueError):
obj._targetscan_ts_type(0, 'A')
def test_properties(self):
self.assertAlmostEqual(
targetscan.mmTargetScan(seed=self.seed).tgs_au,
-0.0501892775521989,
places=5
)
self.assertAlmostEqual(
targetscan.mmTargetScan(seed=self.seed).tgs_position,
-0.01525600000000000,
places=5
)
self.assertAlmostEqual(
targetscan.mmTargetScan(seed=self.seed).tgs_pairing3p,
0.051500000000000004,
places=5
)
self.assertAlmostEqual(
targetscan.mmTargetScan(seed=self.seed).tgs_score,
-0.07732527755219891,
places=5
)
def test_eval_tgs_pairing3p(self):
obj = targetscan.mmTargetScan(seed=self.seed)
with self.assertRaises(AttributeError):
obj.tgs_pairing3ps
t1 = obj._eval_tgs_pairing3p()
r1 = [0.003119999999999999, 0.051500000000000004]
self.assertAlmostEqualList(t1, r1)
self.assertAlmostEqualList(obj.tgs_pairing3ps, r1)
self.assertAlmostEqual(obj.tgs_pairing3p, max(r1), places=5)
def test_eval_tgs_position(self):
obj = targetscan.mmTargetScan(seed=self.seed)
with self.assertRaises(AttributeError):
obj.tgs_positions
t1 = obj._eval_tgs_position()
r1 = [-0.015256000000000002, -0.031904]
self.assertAlmostEqualList(t1, r1)
self.assertAlmostEqualList(obj.tgs_positions, r1)
self.assertAlmostEqual(obj.tgs_position, max(r1), places=5)
def test_eval_tgs_au(self):
obj = targetscan.mmTargetScan(seed=self.seed)
with self.assertRaises(AttributeError):
obj.tgs_aus
t1 = obj._eval_tgs_au()
r1 = [-0.0501892775521989, -0.11318565255796981]
self.assertAlmostEqualList(t1, r1)
self.assertAlmostEqualList(obj.tgs_aus, r1)
self.assertAlmostEqual(obj.tgs_au, max(r1), places=5)
def __init_targetscan(self, **args): self._target_scan = targetscan.mmTargetScan(self._seed, **args)