def test_from_components_no_copy(self):
a = Component('ABCDE', id='a')
f = Component('FGH')
i = Component('IJKLMNOPQ', id='i')
combined = Component.combine(a, f, i)
self.assertEqual('ABCDEFGHIJKLMNOPQ', str(combined.seq))
qualifiers = {'mol_type': 'other DNA', 'organism': None}
self.assertEqual([
Feature(a,
FeatureLocation(0, 5),
type='source',
qualifiers=qualifiers,
ref='a'),
Feature(
f, FeatureLocation(5,
8), type='source', qualifiers=qualifiers),
Feature(i,
FeatureLocation(8, 17),
type='source',
qualifiers=qualifiers,
ref='i')
], list(combined.features))
def test_export_combined(self):
c1 = Component(Seq('AGAGAGAGAGA', alphabet=DNAAlphabet()), annotations={'organism': 'Predator'})
c2 = Component(Seq('CGCGCGCCGCGCGCGCG', alphabet=DNAAlphabet()), annotations={'organism': 'Alien'})
c3 = Component(Seq('AAAAAAAAAAATTTTAA', alphabet=DNAAlphabet()))
c123 = Component.combine(c1, c2, c3)
record = GenbankConverter.to_seq_record(c123)
self.assertEqual(open('fixtures/c123.gb').read(), record.format('genbank'))
def test_from_components_copy(self):
co_1 = Component(Seq('AAATTTAAA'))
co_1.features.add(FeatureLocation(3, 6), type='repeat', qualifiers={'name': 'ts'})
co_2 = Component(Seq('G' * 10))
co_2.features.add(FeatureLocation(0, 10), type='repeat', qualifiers={'name': 'gs'})
combined = Component.combine(co_1, co_2, copy_features=True)
self.assertEqual('AAATTTAAAGGGGGGGGGG', str(combined.seq))
self.assertEqual([Feature(combined, FeatureLocation(3, 6), type='repeat', qualifiers={'name': 'ts'}),
Feature(combined, FeatureLocation(9, 19), type='repeat', qualifiers={'name': 'gs'})], list(combined.features))
def test_export_combined(self):
c1 = Component(Seq('AGAGAGAGAGA', alphabet=DNAAlphabet()),
annotations={'organism': 'Predator'})
c2 = Component(Seq('CGCGCGCCGCGCGCGCG', alphabet=DNAAlphabet()),
annotations={'organism': 'Alien'})
c3 = Component(Seq('AAAAAAAAAAATTTTAA', alphabet=DNAAlphabet()))
c123 = Component.combine(c1, c2, c3)
record = GenbankConverter.to_seq_record(c123)
self.assertEqual(
open('fixtures/c123.gb').read(), record.format('genbank'))
def test_from_components_no_copy(self):
a = Component('ABCDE', id='a')
f = Component('FGH')
i = Component('IJKLMNOPQ', id='i')
combined = Component.combine(a, f, i)
self.assertEqual('ABCDEFGHIJKLMNOPQ', str(combined.seq))
qualifiers = {'mol_type': 'other DNA', 'organism': None}
self.assertEqual([Feature(a, FeatureLocation(0, 5), type='source', qualifiers=qualifiers, ref='a'),
Feature(f, FeatureLocation(5, 8), type='source', qualifiers=qualifiers),
Feature(i, FeatureLocation(8, 17), type='source', qualifiers=qualifiers, ref='i')],
list(combined.features))
def test_from_components_copy(self):
co_1 = Component(Seq('AAATTTAAA'))
co_1.features.add(FeatureLocation(3, 6),
type='repeat',
qualifiers={'name': 'ts'})
co_2 = Component(Seq('G' * 10))
co_2.features.add(FeatureLocation(0, 10),
type='repeat',
qualifiers={'name': 'gs'})
combined = Component.combine(co_1, co_2, copy_features=True)
self.assertEqual('AAATTTAAAGGGGGGGGGG', str(combined.seq))
self.assertEqual([
Feature(combined,
FeatureLocation(3, 6),
type='repeat',
qualifiers={'name': 'ts'}),
Feature(combined,
FeatureLocation(9, 19),
type='repeat',
qualifiers={'name': 'gs'})
], list(combined.features))