def test_locus_add_codon(self):
c = models.Codon()
l = models.Locus()
for codon in [c, 'atg']:
l.add_codon(codon)
self.assertEqual(len(l.codons), 2)
self.assertEqual(l.codons[0].seq, '---')
self.assertEqual(l.codons[1].seq, 'atg')
def test_locus_init(self):
l = models.Locus()
self.assertEqual(l.loc, 0)
self.assertEqual(l.loc_aa, 1)
self.assertEqual(l.__str__(), '<Locus >')
l = models.Locus(codons=[models.Codon(), 'atg'])
self.assertEqual(len(l.codons), 2)
self.assertEqual(l.codons[0].seq, '---')
self.assertEqual(l.codons[1].seq, 'atg')
def test_make_sub_from_p(self):
q = models.goldman_Q(scale_q=False)
p = models.convert_q_to_p(q, t=10)
p_cumsum, p_codons, p_cumsum_dict = models.get_cumulative_p(p, return_dict=True)
old_codon_seq = 'aaa'
old_codon = models.Codon(seq=old_codon_seq)
models.make_sub_from_p(old_codon, p_cumsum_dict)
self.assertEqual(len(old_codon.seq), 3)
allowed_letters = 'atgc'
for i in old_codon.seq:
self.assertIn(i, allowed_letters)
def test_make_subs_in_locus(self):
q = models.goldman_Q(scale_q=False)
p = models.convert_q_to_p(q, t=10)
p_cumsum, p_codons, p_cumsum_dict = models.get_cumulative_p(p, return_dict=True)
old_codon_seq = 'aaa'
old_codons = [models.Codon(seq=old_codon_seq)]*2
locus = models.Locus(codons=old_codons)
old_seq = locus.sequence
while locus.sequence == old_seq:
models.make_subs_in_locus(locus, p_cumsum_dict)
self.assertNotEqual(locus.history, [])
def test_locus_cannot_add_spurious_codons(self):
c = models.Codon()
with self.assertRaises(ValueError):
l = models.Locus(codons=[c, 'abc'])
def test_codon_delete(self):
c = models.Codon(seq='atg')
self.assertEqual(c.seq, 'atg')
c.delete()
self.assertEqual(c.seq, '---')
def test_codon_seq_validation(self):
c = models.Codon()
c.seq = 'a'
self.assertEqual(c.seq, 'a--')
def test_codon_init(self):
c = models.Codon()
self.assertEqual(c.__str__(), '<Codon --->')
def test_make_indel_force_insertion(self):
c = models.Codon(seq='atg')
l = models.Locus(codons=[c])
models.make_indel(l, index=0, ti_td=1e12, codon_freq=None)
self.assertEqual(len(l.codons), 2)
self.assertFalse(any(i.seq == '---' for i in l.codons))
def test_make_indel_force_deletion(self):
c = models.Codon(seq='atg')
l = models.Locus(codons=[c])
models.make_indel(l, index=0, ti_td=0.0, codon_freq=None)
self.assertIn('---', [i.seq for i in l.codons])