def test_concat(self):
'''Tests concat method.'''
directory = os.path.dirname(os.path.realpath(__file__))
dna2 = sbol_utils.read(os.path.join(directory, 'sbol2.xml'))
dna3 = sbol_utils.read(os.path.join(directory, 'sbol3.xml'))
concat_dna = test_sbol_utils.round_trip(dna_utils.concat([dna2, dna3]))
self.assertFalse(concat_dna['features'][0]['forward'])
self.assertEqual(len(dna2['features']) + len(dna3['features']),
len(concat_dna['features']))
def test_concat(self):
'''Tests concat method.'''
directory = os.path.dirname(os.path.realpath(__file__))
dna2 = sbol_utils.read(os.path.join(directory, 'sbol2.xml'))
dna3 = sbol_utils.read(os.path.join(directory, 'sbol3.xml'))
concat_dna = test_sbol_utils.round_trip(dna_utils.concat([dna2, dna3]))
self.assertFalse(concat_dna['features'][0]['forward'])
self.assertEqual(
len(dna2['features']) + len(dna3['features']),
len(concat_dna['features']))
def test_json(self):
'''Tests json roundtrip.'''
directory = os.path.dirname(os.path.realpath(__file__))
dna1 = sbol_utils.read(os.path.join(directory, 'sbol.xml'))
params = json.loads(json.dumps(dna1))
dna2 = dna_utils.DNA(**params)
self.assertEqual(dna1, dna2)
def test_json(self):
'''Tests json roundtrip.'''
directory = os.path.dirname(os.path.realpath(__file__))
dna1 = sbol_utils.read(os.path.join(directory, 'sbol.xml'))
params = json.loads(json.dumps(dna1))
dna2 = dna_utils.DNA(**params)
self.assertEqual(dna1, dna2)
def _get_apply_restrict_site_dnas(restr, circ):
'''Tests apply_restriction_site method.'''
directory = os.path.dirname(os.path.realpath(__file__))
par = sbol_utils.read(os.path.join(directory, 'restrict.xml'))
return par, [
test_sbol_utils.round_trip(dna)
for dna in dna_utils.apply_restricts(par, [restr], circ)
]
def __get_dna(self, ice_id):
'''Gets the sequence ICE entry.'''
url = self.__url + '/rest/file/' + self.__get_ice_number(ice_id) + \
'/sequence/sbol1?sid=' + self.__sid
temp_file = tempfile.NamedTemporaryFile(delete=False)
with codecs.open(temp_file.name, 'w', 'utf-8') as text_file:
text_file.write(net_utils.get(url))
return sbol_utils.read(temp_file.name)
def _get_apply_restrict_site_dnas(restr, circ):
'''Tests apply_restriction_site method.'''
directory = os.path.dirname(os.path.realpath(__file__))
par = sbol_utils.read(os.path.join(directory, 'restrict.xml'))
return par, [test_sbol_utils.round_trip(dna)
for dna in dna_utils.apply_restricts(par, [restr], circ)]
def test_copy(self):
'''Tests copy method.'''
directory = os.path.dirname(os.path.realpath(__file__))
dna1 = sbol_utils.read(os.path.join(directory, 'sbol.xml'))
dna2 = test_sbol_utils.round_trip(dna1.copy())
self.assertEqual(dna1, dna2)
def test_copy(self):
'''Tests copy method.'''
directory = os.path.dirname(os.path.realpath(__file__))
dna1 = sbol_utils.read(os.path.join(directory, 'sbol.xml'))
dna2 = test_sbol_utils.round_trip(dna1.copy())
self.assertEqual(dna1, dna2)
def _read(filename):
'''Reads sbol file.'''
directory = os.path.dirname(os.path.realpath(__file__))
return sbol_utils.read(os.path.join(directory, filename))
def _read(filename):
'''Reads sbol file.'''
directory = os.path.dirname(os.path.realpath(__file__))
return sbol_utils.read(os.path.join(directory, filename))
def round_trip(dna):
'''Writes / reads DNA object, via SBOL export / import.'''
tmp = tempfile.NamedTemporaryFile()
sbol_utils.write(dna, tmp.name)
return sbol_utils.read(tmp.name)
def test(self):
'''Tests round trip equality.'''
directory = os.path.dirname(os.path.realpath(__file__))
dna1 = sbol_utils.read(os.path.join(directory, 'sbol.xml'))
dna2 = round_trip(dna1)
self.assertEqual(dna1, dna2)
