def test_symmetric_difference_update(self):
syn_1 = 'a'
syn_2 = 'b'
syn_3 = 'c'
syns_1 = core.SynonymSet([syn_1, syn_2])
syns_2 = core.SynonymSet([syn_1, syn_3])
syns_1.symmetric_difference_update(syns_2)
self.assertEqual(syns_1, core.SynonymSet([syn_2, syn_3]))
syns_1 = core.SynonymSet([syn_1, syn_2])
syns_2 = set([syn_1, syn_3])
syns_1.symmetric_difference_update(syns_2)
self.assertEqual(syns_1, core.SynonymSet([syn_2, syn_3]))
with self.assertRaises(TypeError):
syns_1.symmetric_difference_update(0)
def test_synonyms_setter(self):
base = core.Base()
base.synonyms = core.SynonymSet()
base.synonyms = set(['A'])
base.synonyms = ['A']
with self.assertRaises(ValueError):
base.synonyms = None
with self.assertRaises(ValueError):
base.synonyms = 'A'
def test_update(self):
syn_1 = 'a'
syn_2 = 'b'
syn_3 = 'c'
syns = core.SynonymSet()
syns.update([syn_1, syn_2])
self.assertEqual(len(syns), 2)
with self.assertRaises(ValueError):
syns.update([0])
def test_add(self):
syn_1 = 'a'
syn_2 = 'b'
syn_3 = 'c'
syns = core.SynonymSet()
syns.add(syn_1)
syns.add(syn_2)
syns.add(syn_3)
self.assertEqual(len(syns), 3)
with self.assertRaises(ValueError):
syns.add(0)
with self.assertRaises(ValueError):
syns.add(None)
with self.assertRaises(ValueError):
syns.add('')
def test_constructor(self):
syn_1 = 'a'
syn_2 = 'b'
syn_3 = 'c'
syns = core.SynonymSet()
self.assertEqual(len(syns), 0)
syns = core.SynonymSet([syn_1, syn_2, syn_3])
self.assertEqual(len(syns), 3)
with self.assertRaises(ValueError):
core.SynonymSet('')
with self.assertRaises(ValueError):
core.SynonymSet('a')
with self.assertRaises(ValueError):
core.SynonymSet([''])
with self.assertRaises(ValueError):
core.SynonymSet([0])
with self.assertRaises(ValueError):
core.SynonymSet([None])
def test_from_str(self):
self.assertTrue(dna.DnaForm.from_str('AAA').is_equal(dna.DnaForm([
dna.dna_alphabet.A, dna.dna_alphabet.A, dna.dna_alphabet.A,
])))
self.assertTrue(dna.DnaForm.from_str('ACTG').is_equal(dna.DnaForm([
dna.dna_alphabet.A, dna.dna_alphabet.C, dna.dna_alphabet.T, dna.dna_alphabet.G,
])))
with self.assertRaisesRegex(ValueError, 'not in alphabet'):
self.assertTrue(dna.DnaForm.from_str('UAA').is_equal(dna.DnaForm([
dna.dna_alphabet.A, dna.dna_alphabet.A, dna.dna_alphabet.A,
])))
self.assertTrue(dna.DnaForm.from_str(
'AA[id: "dI"'
+ ' | name: "2\'-deoxyinosine"'
+ ' | synonym: "2\'-deoxyinosine, 9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-9H-purin-6-ol"'
+ ' | identifier: chebi/CHEBI:28997'
+ ' | structure: ' + dIMP_inchi
+ ' | delta-mass: -2.5'
+ ' | delta-charge: 3'
+ ' | position: 3-5'
+ ' | comments: "A purine 2\'-deoxyribonucleoside that is inosine ..."]A').is_equal(dna.DnaForm([
dna.dna_alphabet.A,
dna.dna_alphabet.A,
core.Base(
id='dI',
name="2'-deoxyinosine",
synonyms=core.SynonymSet(
["2'-deoxyinosine, 9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-9H-purin-6-ol"]),
identifiers=core.IdentifierSet([core.Identifier('chebi', 'CHEBI:28997')]),
structure=dIMP_inchi,
delta_mass=-2.5,
delta_charge=3,
start_position=3,
end_position=5,
comments="A purine 2'-deoxyribonucleoside that is inosine ...",
),
dna.dna_alphabet.A,
])))
self.assertTrue(dna.DnaForm.from_str(
'AA[id: "dI"'
' | position: 3-]A').is_equal(dna.DnaForm([
dna.dna_alphabet.A,
dna.dna_alphabet.A,
core.Base(
id='dI',
start_position=3,
end_position=None,
),
dna.dna_alphabet.A,
])))
self.assertTrue(dna.DnaForm.from_str(
'AA[id: "dI"'
' | position: -5]A').is_equal(dna.DnaForm([
dna.dna_alphabet.A,
dna.dna_alphabet.A,
core.Base(
id='dI',
start_position=None,
end_position=5,
),
dna.dna_alphabet.A,
])))
with self.assertRaisesRegex(ValueError, 'cannot be repeated'):
dna.DnaForm.from_str(
'AA[id: "dI"'
' | name: "2\'-deoxyinosine"'
' | name: "2\'-deoxyinosine"]A')