def test_circular_sequences(self): """Deal with cutting circular sequences. """ parts = EcoRI.catalyse(self.ecosite_seq, linear=False) self.assertEqual(len(parts), 1) locations = EcoRI.search(parts[0], linear=False) self.assertEqual(locations, [1])
def find_EcoRi (DNA_sequence): "Find EcoRi restriction site and give position of sticky ends" pos=[] eco_start= EcoRI.search(DNA_sequence) for entry in eco_start: eco_end = entry + 4 pos.append(entry) pos.append(eco_end) return(pos);
def test_eco_cutting(self): """Test basic cutting with EcoRI.""" self.assertEqual(EcoRI.site, 'GAATTC') self.assertFalse(EcoRI.is_blunt()) self.assertTrue(EcoRI.is_5overhang()) self.assertFalse(EcoRI.is_3overhang()) self.assertEqual(EcoRI.elucidate(), "G^AATT_C") self.assertEqual(EcoRI.search(self.ecosite_seq), [6]) parts = EcoRI.catalyse(self.ecosite_seq) self.assertEqual(len(parts), 2) self.assertEqual(str(parts[1]), "AATTCAAAA") parts = EcoRI.catalyze(self.ecosite_seq) self.assertEqual(len(parts), 2)
def test_sequence_object(self): """Test if sequence must be a Seq or MutableSeq object.""" with self.assertRaises(TypeError): seq = FormattedSeq('GATC') seq = FormattedSeq(Seq('TAGC')) seq = FormattedSeq(MutableSeq('AGTC')) seq = FormattedSeq(seq) with self.assertRaises(TypeError): EcoRI.search('GATC') EcoRI.search(Seq('ATGC')) EcoRI.search(MutableSeq('TCAG'))
def test_sequence_object(self): """Test if sequence must be a Seq or MutableSeq object.""" with self.assertRaises(TypeError): seq = FormattedSeq('GATC') seq = FormattedSeq(Seq('TAGC')) seq = FormattedSeq(MutableSeq('AGTC')) seq = FormattedSeq(seq) with self.assertRaises(TypeError): EcoRI.search('GATC') EcoRI.search(Seq('ATGC')) EcoRI.search(MutableSeq('TCAG'))
def test_circular_sequences(self): """Deal with cutting circular sequences.""" parts = EcoRI.catalyse(self.ecosite_seq, linear=False) self.assertEqual(len(parts), 1) locations = EcoRI.search(parts[0], linear=False) self.assertEqual(locations, [1]) parts = KpnI.catalyse(self.kpnsite_seq, linear=False) self.assertEqual(len(parts), 1) locations = KpnI.search(parts[0], linear=False) self.assertEqual(locations, [1]) parts = SmaI.catalyse(self.smasite_seq, linear=False) self.assertEqual(len(parts), 1) locations = SmaI.search(parts[0], linear=False) self.assertEqual(locations, [1]) self.assertEqual( EarI.search(FormattedSeq(Seq('CTCTTCAAAAA')), linear=False), [8]) self.assertEqual( SnaI.search(FormattedSeq(Seq('GTATACAAAAA')), linear=False), [1])
def test_circular_sequences(self): """Deal with cutting circular sequences.""" parts = EcoRI.catalyse(self.ecosite_seq, linear=False) self.assertEqual(len(parts), 1) locations = EcoRI.search(parts[0], linear=False) self.assertEqual(locations, [1]) parts = KpnI.catalyse(self.kpnsite_seq, linear=False) self.assertEqual(len(parts), 1) locations = KpnI.search(parts[0], linear=False) self.assertEqual(locations, [1]) parts = SmaI.catalyse(self.smasite_seq, linear=False) self.assertEqual(len(parts), 1) locations = SmaI.search(parts[0], linear=False) self.assertEqual(locations, [1]) self.assertEqual(EarI.search(FormattedSeq(Seq('CTCTTCAAAAA')), linear=False), [8]) self.assertEqual(SnaI.search(FormattedSeq(Seq('GTATACAAAAA')), linear=False), [1])
def test_eco_cutting(self): """Test basic cutting with EcoRI (5'overhang).""" self.assertEqual(EcoRI.site, 'GAATTC') self.assertTrue(EcoRI.cut_once()) self.assertFalse(EcoRI.is_blunt()) self.assertTrue(EcoRI.is_5overhang()) self.assertFalse(EcoRI.is_3overhang()) self.assertEqual(EcoRI.overhang(), "5' overhang") self.assertTrue(EcoRI.is_defined()) self.assertFalse(EcoRI.is_ambiguous()) self.assertFalse(EcoRI.is_unknown()) self.assertTrue(EcoRI.is_palindromic()) self.assertTrue(EcoRI.is_comm()) self.assertIn('Life Technologies', EcoRI.supplier_list()) self.assertEqual(EcoRI.elucidate(), "G^AATT_C") self.assertEqual(EcoRI.search(self.ecosite_seq), [6]) self.assertEqual(EcoRI.characteristic(), (1, -1, None, None, 'GAATTC')) parts = EcoRI.catalyse(self.ecosite_seq) self.assertEqual(len(parts), 2) self.assertEqual(str(parts[1]), "AATTCAAAA") parts = EcoRI.catalyze(self.ecosite_seq) self.assertEqual(len(parts), 2)
def test_eco_cutting(self): """Test basic cutting with EcoRI (5'overhang).""" self.assertEqual(EcoRI.site, 'GAATTC') self.assertTrue(EcoRI.cut_once()) self.assertFalse(EcoRI.is_blunt()) self.assertTrue(EcoRI.is_5overhang()) self.assertFalse(EcoRI.is_3overhang()) self.assertEqual(EcoRI.overhang(), "5' overhang") self.assertTrue(EcoRI.is_defined()) self.assertFalse(EcoRI.is_ambiguous()) self.assertFalse(EcoRI.is_unknown()) self.assertTrue(EcoRI.is_palindromic()) self.assertTrue(EcoRI.is_comm()) self.assertIn('Life Technologies', EcoRI.supplier_list()) self.assertEqual(EcoRI.elucidate(), "G^AATT_C") self.assertEqual(EcoRI.search(self.ecosite_seq), [6]) self.assertEqual(EcoRI.characteristic(), (1, -1, None, None, 'GAATTC')) parts = EcoRI.catalyse(self.ecosite_seq) self.assertEqual(len(parts), 2) self.assertEqual(str(parts[1]), "AATTCAAAA") parts = EcoRI.catalyze(self.ecosite_seq) self.assertEqual(len(parts), 2)