def test_str(self):
base = core.Base()
base.id = 'dAMP'
self.assertEqual(str(base), '[id: "dAMP"]')
base.name = 'deoxyadenosine monophosphate'
self.assertEqual(str(base), '[id: "dAMP" | name: "deoxyadenosine monophosphate"]')
base.synonyms = set(['A', 'dAMP'])
self.assertIn(' | synonym: "A"', str(base))
self.assertIn(' | synonym: "dAMP"', str(base))
base.identifiers = set([core.Identifier('chebi', 'CHEBI:58245'), core.Identifier('biocyc.compound', 'DAMP')])
self.assertIn(' | identifier: chebi/CHEBI:58245', str(base))
self.assertIn(' | identifier: biocyc.compound/DAMP', str(base))
base.structure = dAMP_inchi
self.assertIn(' | structure: {}]'.format(dAMP_inchi), str(base))
base.delta_mass = 1.
base.delta_charge = -1
self.assertIn(' | delta-mass: 1', str(base))
self.assertIn(' | delta-charge: -1', str(base))
base.start_position = 3
self.assertIn(' | position: 3-]', str(base))
base.end_position = 5
self.assertIn(' | position: 3-5]', str(base))
base.start_position = None
self.assertIn(' | position: -5]', str(base))
base.comments = 'help "me"'
self.assertIn(' | comments: "help \\"me\\""', str(base))
def test_set(self):
id_1 = core.Identifier('ec-code', '1.1.1.2')
id_2 = core.Identifier('ec-code', '1.1.1.2')
id_3 = core.Identifier('ec-code', '1.1.1.1')
id_4 = core.Identifier('kegg.compound', '1.1.1.2')
ids = set([id_1, id_2, id_3, id_4])
self.assertEqual(len(ids), 3)
def test_hash(self):
id_1 = core.Identifier('ec-code', '1.1.1.2')
id_2 = core.Identifier('ec-code', '1.1.1.2')
id_3 = core.Identifier('ec-code', '1.1.1.1')
id_4 = core.Identifier('kegg.compound', '1.1.1.2')
self.assertEqual(id_1.__hash__(), id_2.__hash__())
self.assertNotEqual(id_1.__hash__(), id_3.__hash__())
self.assertNotEqual(id_1.__hash__(), id_4.__hash__())
def test_identifiers_setter(self):
base = core.Base()
base.identifiers = core.IdentifierSet()
base.identifiers = set([core.Identifier('ns', 'id')])
base.identifiers = [core.Identifier('ns', 'id')]
with self.assertRaises(ValueError):
base.identifiers = None
with self.assertRaises(ValueError):
base.identifiers = 'A'
with self.assertRaises(TypeError):
base.identifiers = core.Identifier('ns', 'id')
def test_update(self):
id_1 = core.Identifier('ec-code', '1.1.1.2')
id_2 = core.Identifier('ec-code', '1.1.1.1')
id_3 = core.Identifier('kegg.compound', '1.1.1.2')
ids = core.IdentifierSet()
ids.update([id_1, id_2])
self.assertEqual(len(ids), 2)
with self.assertRaises(ValueError):
ids.update([('ec-code', '1.1.1.2')])
def test_eq(self):
id_1 = core.Identifier('ec-code', '1.1.1.2')
id_2 = core.Identifier('ec-code', '1.1.1.2')
id_3 = core.Identifier('ec-code', '1.1.1.1')
id_4 = core.Identifier('kegg.compound', '1.1.1.2')
self.assertEqual(id_1, id_2)
self.assertEqual(id_2, id_1)
self.assertNotEqual(id_1, id_3)
self.assertNotEqual(id_1, id_4)
self.assertNotEqual(id_1, '')
self.assertNotEqual(id_1, 0)
def test_constructor(self):
id_1 = core.Identifier('ec-code', '1.1.1.2')
id_2 = core.Identifier('ec-code', '1.1.1.1')
id_3 = core.Identifier('kegg.compound', '1.1.1.2')
ids = core.IdentifierSet()
self.assertEqual(len(ids), 0)
ids = core.IdentifierSet([id_1, id_2, id_3])
self.assertEqual(len(ids), 3)
with self.assertRaises(ValueError):
core.IdentifierSet(['ec-code'])
def test_add(self):
id_1 = core.Identifier('ec-code', '1.1.1.2')
id_2 = core.Identifier('ec-code', '1.1.1.1')
id_3 = core.Identifier('kegg.compound', '1.1.1.2')
ids = core.IdentifierSet()
ids.add(id_1)
ids.add(id_2)
ids.add(id_3)
self.assertEqual(len(ids), 3)
with self.assertRaises(ValueError):
ids.add(('ec-code', '1.1.1.2'))
def test_symmetric_difference_update(self):
id_1 = core.Identifier('ec-code', '1.1.1.2')
id_2 = core.Identifier('ec-code', '1.1.1.1')
id_3 = core.Identifier('kegg.compound', '1.1.1.2')
ids_1 = core.IdentifierSet([id_1, id_2])
ids_2 = core.IdentifierSet([id_1, id_3])
ids_1.symmetric_difference_update(ids_2)
self.assertEqual(ids_1, core.IdentifierSet([id_2, id_3]))
ids_1 = core.IdentifierSet([id_1, id_2])
ids_2 = set([id_1, id_3])
ids_1.symmetric_difference_update(ids_2)
self.assertEqual(ids_1, core.IdentifierSet([id_2, id_3]))
with self.assertRaises(TypeError):
ids_1.symmetric_difference_update(id_1)
def test_init(self):
identifiers = set([
core.Identifier('chebi', 'CHEBI:58245'),
core.Identifier('pubchem.compound', '22848660'),
core.Identifier('metacyc.compound', 'DAMP'),
])
synonyms = set(['A', 'dAMP', 'deoxyadenosine monophosphate'])
base = core.Base(id='dAMP', name='deoxyadenosine monophosphate', synonyms=synonyms, identifiers=identifiers,
structure=dAMP_inchi, delta_mass=1., delta_charge=-1, start_position=2, end_position=10, comments='Long string')
self.assertEqual(base.id, 'dAMP')
self.assertEqual(base.name, 'deoxyadenosine monophosphate')
self.assertEqual(base.synonyms, synonyms)
self.assertEqual(base.identifiers, identifiers)
self.assertEqual(base.get_inchi(), dAMP_inchi)
self.assertEqual(base.delta_mass, 1.)
self.assertEqual(base.delta_charge, -1)
self.assertEqual(base.start_position, 2)
self.assertEqual(base.end_position, 10)
self.assertEqual(base.comments, 'Long string')
def test_constructor(self):
id = core.Identifier('ec-code', '1.1.1.2')
self.assertEqual(id.ns, 'ec-code')
self.assertEqual(id.id, '1.1.1.2')
id = core.Identifier('kegg.compound', 'C00001')
self.assertEqual(id.ns, 'kegg.compound')
self.assertEqual(id.id, 'C00001')
id = core.Identifier('chebi', 'CHEBI:57566')
self.assertEqual(id.ns, 'chebi')
self.assertEqual(id.id, 'CHEBI:57566')
id = core.Identifier('metacyc.compound', 'DAMP')
self.assertEqual(id.ns, 'metacyc.compound')
self.assertEqual(id.id, 'DAMP')
id = core.Identifier('pubchem.compound', '22848660')
self.assertEqual(id.ns, 'pubchem.compound')
self.assertEqual(id.id, '22848660')
with self.assertRaises(ValueError):
id.ns = ''
with self.assertRaises(ValueError):
id.ns = '"pubchem"'
with self.assertRaises(ValueError):
id.ns = 0
with self.assertRaises(ValueError):
id.ns = None
with self.assertRaises(ValueError):
id.id = ''
with self.assertRaises(ValueError):
id.id = 0
with self.assertRaises(ValueError):
id.id = None
with self.assertRaises(ValueError):
id.id = '"22848660"'
self.assertEqual(id.ns, 'pubchem.compound')
self.assertEqual(id.id, '22848660')
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')