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_load_fasta(self):
with self.assertRaises(IOError):
utils.load_fasta("NONEXISTENT.fa")
fa = utils.load_fasta('tests/input/NM_024573.fa')
fa_content = {
'NM_024573': (
'CUUGAUUUAGGAGCUCUCAGUUGCAUAGAAAGAUCUGGUGAGCACCUUUUCAUCCCCAGAAAAGGAGCAC'
'GUGAAUUGAGUCGCCUGGCGGCUCUGUACGCGCUCAGGGAAGCUUAGCUUCUUGGUGCCCAUCUACGUGC'
'ACUGGAUGAUUUUUCUUUUGAACAUUUUGCCCCACUACACUGUUUUGGGGAUAGCUGGGUUAAGCAAGUU'
'AAAGAUAUUUACAUUUAUAUUGGAAUUUUAGCAACUUUUUUUCAGGUUAAAUAUAUAAUUUCAAGUGCUU'
'UUAAUGAACUUAUUUUUAAUUGGCUAGGGAGCAAAAAAUAAGUGAGUUCUGCUUUUAGUUAGUUAACCUU'
'GUUCUUUUCUUAAAUAGUACACUGCAUGGUAUUUAAUAUUCCAGGAAGCAUGGGAUUUUAUUUUGCUUGA'
'UUUUGGGCACAUGAAAUAAUAGCUCUAGGAAAAUGCGCAUCUUAAUGACUCUUUGUAAAGAGAGGCAUUU'
'CUUACAACUGUGAUGUUUGCUUACAUAAAAGUUACCUCAUAAGUUAAUUCUAACUUUUAUUCUUGAAUUU'
'UAUUUCAUUUCAAUAGCUUGUUUCAUUUGCACGCCUUUGUAUUUUGAUUGACCUGUAGAAUGGAUGUUAG'
'GAAACUCAAAAUUGAACACAGUGAAACAAAUGGUAUUUGAAGAAAUGUAAUAUCUUUUAUAUUCUAUUUA'
'UGAUAUCCAUAAUCAAAUGAGAUUAUUUUACCACAUAAAUGUUUUAAAUAUCAGAUUUUUAGUUUGCAGU'
'UUUAGGAAAAUGCUUUAGAUAGAAAAGGUUCUUAUGCAUUGAAUUUGGAGUACUACCAACAAUGAAUGAA'
'UUUAUUUUUUAUAUUCUUACACAUUUUAUUGGUCAUUGUCACAGAUAGUAAAUACUAAAAAUUUCAGGUC'
'AGUUUGUUUUGAAACUGAAAUUGGAAAUAAAUCUGGAAAUGUUUUGUUGCACUAAAAUAAUAAAAUGAAU'
'UGUACUG'
)
}
self.assertIsInstance(fa, dict)
self.assertEqual(fa.keys(), fa_content.keys())
self.assertEqual(fa['NM_024573'], fa_content['NM_024573'])
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()
