def __init_seed(self, **args):
arg_init = {
'target_seq': self.seq_mrn,
'mirna_seq': self.seq_mir
}
args.update(arg_init)
self._seed = seed.mmSeed(**args)
def setUp(self):
_mirs = utils.load_fasta('tests/input/hsa-miR-30a-3p.fa')
_mrnas = utils.load_fasta('tests/input/NM_024573.fa')
args = {
'target_seq': _mrnas['NM_024573'],
'mirna_seq': _mirs['hsa-miR-30a-3p'],
}
self.seed = seed.mmSeed(**args)
self.seed.find_potential_targets_with_seed()
def test_init(self):
with self.assertRaises(KeyError):
seed.mmSeed()
seed.mmSeed(target_seq="AUGC")
seed.mmSeed(mirna_seq="AUGC")
temp = seed.mmSeed(target_seq="augcaugc", mirna_seq="augc")
self.assertIsInstance(temp, seed.mmSeed)
self.assertEqual(temp.target_seq, "AUGCAUGC")
self.assertEqual(temp.mirna_seq, "AUGC")
self.assertEqual(temp.min_target_length, len("AUGC"))
self.assertEqual(temp.len_mirna_seq, len("AUGC"))
self.assertEqual(temp.len_target_seq, len("AUGCAUGC"))
temp2 = seed.mmSeed(target_seq="augc", mirna_seq="augc",
min_target_length=2)
self.assertEqual(temp2.min_target_length, 2)
def test_find_potential_targets_with_seed(self):
args = {
'target_seq': self._mrnas['NM_024573'],
'mirna_seq': self._mirs['hsa-miR-30a-3p'],
}
obj = seed.mmSeed(**args)
self.assertIsInstance(obj, seed.mmSeed)
r1 = obj.find_potential_targets_with_seed()
ar1 = {
'end_sites': [931, 931],
'seed_lengths': [7, 6],
'pairings': [[0, 2, 3, 4, 5, 6, 7, 8], [0, 2, 3, 4, 5, 6, 7]],
'nb_mismatches_except_gu_wobbles': [0, 0],
'nb_gu_wobbles': [0, 0]
}
self.assertEqual(r1, ar1)
tar_1 = {
'mirna_start_pairing': 2,
'allowed_lengths': [6, 7, 8],
'allowed_gu_wobbles': {6: 0, 7: 1, 8: 2},
'allowed_mismatches': {6: 0, 7: 0, 8: 0},
'take_best': False,
}
args.update(tar_1)
obj = seed.mmSeed(**args)
tr1 = obj.find_potential_targets_with_seed()
tr1_out = {
'end_sites': [931, 931],
'seed_lengths': [7, 6],
'pairings': [[0, 2, 3, 4, 5, 6, 7, 8], [0, 2, 3, 4, 5, 6, 7]],
'nb_mismatches_except_gu_wobbles': [0, 0],
'nb_gu_wobbles': [0, 0]
}
self.assertEqual(tr1, tr1_out)
self.assertEqual(obj.end_sites, tr1['end_sites'])
self.assertEqual(obj.seed_lengths, tr1['seed_lengths'])
self.assertEqual(obj.pairings, tr1['pairings'])
self.assertEqual(obj.nb_mismatches_except_gu_wobbles,
tr1['nb_mismatches_except_gu_wobbles'])
self.assertEqual(obj.nb_gu_wobbles, tr1['nb_gu_wobbles'])
tar_2 = {
'mirna_start_pairing': 0, #: Changed the pairing start
'allowed_lengths': [6, 7, 8],
'allowed_gu_wobbles': {6: 0, 7: 1, 8: 2},
'allowed_mismatches': {6: 0, 7: 0, 8: 0},
'take_best': False,
}
args.update(tar_2)
obj = seed.mmSeed(**args)
tr2 = obj.find_potential_targets_with_seed()
tr2_out = {
'end_sites': [987, 987, 987],
'seed_lengths': [8, 7, 6],
'pairings': [[], [], []],
'nb_mismatches_except_gu_wobbles': [0, 0, 0],
'nb_gu_wobbles': [0, 0, 0]
}
self.assertEqual(tr2, tr2_out)
self.assertEqual(obj.end_sites, tr2['end_sites'])
self.assertEqual(obj.seed_lengths, tr2['seed_lengths'])
self.assertEqual(obj.pairings, tr2['pairings'])
self.assertEqual(obj.nb_mismatches_except_gu_wobbles,
tr2['nb_mismatches_except_gu_wobbles'])
self.assertEqual(obj.nb_gu_wobbles, tr2['nb_gu_wobbles'])
tar_3 = {
'mirna_start_pairing': 2,
'allowed_lengths': [6, 7, 8],
'allowed_gu_wobbles': {6: 0, 7: 1, 8: 2},
'allowed_mismatches': {6: 0, 7: 0, 8: 0},
'take_best': True, #: Here.
}
args.update(tar_3)
obj = seed.mmSeed(**args)
tr3 = obj.find_potential_targets_with_seed()
tr3_out = {
'end_sites': [931],
'seed_lengths': [7],
'pairings': [[0, 2, 3, 4, 5, 6, 7, 8]],
'nb_mismatches_except_gu_wobbles': [0],
'nb_gu_wobbles': [0]
}
self.assertEqual(tr3, tr3_out)
self.assertEqual(obj.end_sites, tr3['end_sites'])
self.assertEqual(obj.seed_lengths, tr3['seed_lengths'])
self.assertEqual(obj.pairings, tr3['pairings'])
self.assertEqual(obj.nb_mismatches_except_gu_wobbles,
tr3['nb_mismatches_except_gu_wobbles'])
self.assertEqual(obj.nb_gu_wobbles, tr3['nb_gu_wobbles'])
tar_4 = {
'mirna_start_pairing': 2,
'allowed_lengths': [6, 7, 8],
'allowed_gu_wobbles': {6: 0, 7: 1, 8: 2},
'allowed_mismatches': {6: 0, 7: 0, 8: 1},
'take_best': False,
}
args.update(tar_4)
obj = seed.mmSeed(**args)
tr4 = obj.find_potential_targets_with_seed()
tr4_out = {
'end_sites': [937, 931, 931, 931, 796, 236],
'seed_lengths': [8, 8, 7, 6, 8, 8],
'pairings': [
[0, 2, 3, 4, 5, 6, 7, 8, 0],
[0, 2, 3, 4, 5, 6, 7, 8, 0],
[0, 2, 3, 4, 5, 6, 7, 8],
[0, 2, 3, 4, 5, 6, 7],
[0, 2, 3, 4, 5, 0, 7, 8, 9],
[0, 2, 3, 4, 5, 6, 7, 8, 0]
],
'nb_mismatches_except_gu_wobbles': [1, 1, 0, 0, 1, 1],
'nb_gu_wobbles': [2, 0, 0, 0, 1, 2]
}
self.assertEqual(tr4, tr4_out)
self.assertEqual(obj.end_sites, tr4['end_sites'])
self.assertEqual(obj.seed_lengths, tr4['seed_lengths'])
self.assertEqual(obj.pairings, tr4['pairings'])
self.assertEqual(obj.nb_mismatches_except_gu_wobbles,
tr4['nb_mismatches_except_gu_wobbles'])
self.assertEqual(obj.nb_gu_wobbles, tr4['nb_gu_wobbles'])
