def test_mutation_site_different_positions(self):
mutation1 = parse_codon_mutation("A51F")
mutation2 = parse_codon_mutation("A52M")
lst = [mutation1, mutation2]
with self.assertRaises(ValueError) as context:
mut_site = MutationSite(lst)
self.assertTrue("must be on same position" in str(context.exception))
def test_mutation_site_diff_original_aminos(self):
mutation1 = parse_codon_mutation("A51F")
mutation2 = parse_codon_mutation("M51M")
lst = [mutation1, mutation2]
with self.assertRaises(ValueError) as context:
mut_site = MutationSite(lst)
self.assertTrue("must have same amin" in str(context.exception))
def test_get_mutation_string(self):
mutation1 = parse_codon_mutation("A51F")
mutation2 = parse_codon_mutation("A51M")
lst = [mutation1, mutation2]
mut_site = MutationSite(lst)
self.assertEqual("A51A", mut_site.get_mutation_string("A"))
self.assertEqual("A51F", mut_site.get_mutation_string("F"))
self.assertEqual("A51M", mut_site.get_mutation_string("M"))
def test_valid_mutation_site(self):
mutation1 = parse_codon_mutation("A51F")
mutation2 = parse_codon_mutation("A51M")
lst = [mutation1, mutation2]
mut_site = MutationSite(lst)
self.assertEqual(150, mut_site.position)
self.assertEqual("A", mut_site.old_amino)
self.assertIn("F", mut_site.new_aminos)
self.assertIn("M", mut_site.new_aminos)
def test_parse_invalid_position(self):
with self.assertRaises(ValueError) as context:
mutation = parse_codon_mutation("A*F")
self.assertTrue("Position" in str(context.exception))
with self.assertRaises(ValueError) as context:
mutation = parse_codon_mutation("A0F")
self.assertTrue("Position" in str(context.exception))
with self.assertRaises(ValueError) as context:
mutation = parse_codon_mutation("A-12F")
self.assertTrue("positive number" in str(context.exception))
def parse_mutations(self, goi_offset: int) -> List[MutationSite]:
"""
Parses the user input in the format "E32W E32L E49K" and produces multi-amino
mutations in the format of "E32WL E49K"
"""
codon_muts = [parse_codon_mutation(mutation, goi_offset) for mutation in self.mutations]
return create_multi_amino_mutations(codon_muts)
def parse_mutations(self, goi_offset):
return [
parse_codon_mutation(mutation, goi_offset)
for mutation in self.mutations
]
def test_parse_invalid_new_amino(self):
with self.assertRaises(ValueError) as context:
mutation = parse_codon_mutation("A51*")
self.assertTrue(
"Target amino acid is not valid" in str(context.exception))
def test_parse_invalid_orig_amino(self):
with self.assertRaises(ValueError) as context:
mutation = parse_codon_mutation("*51F")
self.assertTrue(
"Original amino acid is not valid" in str(context.exception))
def test_parse_valid_mut(self):
mutation = parse_codon_mutation("A51F")
self.assertEqual("A51F", mutation.original_string)
self.assertEqual("A", mutation.old_amino)
self.assertEqual("F", mutation.new_amino)
self.assertEqual(150, mutation.position)
