def test_infers_within_frame_position(self):
self.assertEqual(
utilities.NucleotideSubstitutionEvent(
"c.3A>G").codon_frame_position(one_based=False),
1,
)
self.assertEqual(
utilities.NucleotideSubstitutionEvent(
"c.3A>G").codon_frame_position(one_based=True),
3,
)
def test_negative_rna_position_error(self):
with self.assertRaises(IndexError):
utilities.NucleotideSubstitutionEvent("r.-100a>u")
def test_parses_negative_positions(self):
nt = utilities.NucleotideSubstitutionEvent("n.-100A>T")
self.assertEqual(nt.position, -100)
def test_parses_prefix(self):
self.assertEqual(
utilities.NucleotideSubstitutionEvent("c.1A>G").prefix, "c")
def test_formats_event_string_correctly(self):
self.assertEqual(
utilities.NucleotideSubstitutionEvent("c.1A>G").event, "1A>G")
self.assertEqual(
utilities.NucleotideSubstitutionEvent("c.1=").event, "1=")
def test_parses_alt_base(self):
self.assertEqual(
utilities.NucleotideSubstitutionEvent("c.1A>G").alt, "G")
self.assertEqual(
utilities.NucleotideSubstitutionEvent("c.1=").alt, None)
def test_infers_silent(self):
self.assertEqual(
utilities.NucleotideSubstitutionEvent("c.1=").silent, True)
def test_parses_ref_base(self):
self.assertEqual(
utilities.NucleotideSubstitutionEvent("c.1A>G").ref, "A")
self.assertEqual(
utilities.NucleotideSubstitutionEvent("c.1=").ref, None)
def test_error_negative_position_when_computing_codon_position(self):
nt = utilities.NucleotideSubstitutionEvent("c.-1A>G")
with self.assertRaises(ValueError):
nt.codon_position()
with self.assertRaises(ValueError):
nt.codon_frame_position()
def test_parses_position(self):
self.assertEqual(
utilities.NucleotideSubstitutionEvent("c.1A>G").position, 1)
self.assertEqual(
utilities.NucleotideSubstitutionEvent("c.-1A>G").position, -1)
def test_strips_ws(self):
self.assertEqual(
utilities.NucleotideSubstitutionEvent(" c.1A>G ").variant,
"c.1A>G")
def test_error_invalid_dna_substitution_syntax(self):
with self.assertRaises(exceptions.InvalidVariantType):
utilities.NucleotideSubstitutionEvent("c.100_101delins")