def test_list_features(self):
c1 = Component('A' * 10)
c1.features.add(FeatureLocation(1, 10), type='repeat')
c2 = Component('T' * 10)
c2.features.add(FeatureLocation(1, 10), type='repeat')
self.assertEqual([Feature(c1, FeatureLocation(1, 10), type='repeat')],
list(c1.features))
self.assertEqual([Feature(c2, FeatureLocation(1, 10), type="repeat")],
list(c2.features))
strain = HaploidOrganism(id='strain')
strain.set('a', c1)
strain.set('b', c2)
strain.set('c', c2)
self.assertEqual(2, len(strain.features))
self.assertEqual(
{
Feature(Component('AAAAAAAAAA'),
FeatureLocation(1, 10),
type="repeat"),
Feature(Component('TTTTTTTTTT'),
FeatureLocation(1, 10),
type="repeat")
}, set(strain.features))
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_mutate_strain(self):
strain = HaploidOrganism(id='strain-1')
genome = Component('A' * 25 + 'C' * 25 + 'G' * 25 + 'T' * 25)
genome.features.add(FeatureLocation(0, 25), type='a')
genome.features.add(FeatureLocation(25, 49), type='c')
feature_3 = genome.features.add(FeatureLocation(50, 74), type='g')
feature_4 = genome.features.add(FeatureLocation(
75, 99), type='t') # FIXME 75 should be possible, no?
strain.set('genome', genome)
mutations = [
SNP(7, 'T'),
SNP(30, 'G'),
Mutation(31, 3, ''),
Mutation(40, new_sequence='GATGA'),
Mutation(feature_3.start, end=feature_3.end - 5),
Mutation(feature_4.start,
end=feature_4.end,
new_sequence=Seq('GAGAGA'))
]
new_genome = strain.components['genome'].mutate(mutations)
new_strain = HaploidOrganism('strain-2', parent=strain)
new_strain.set('genome', new_genome) # sets genome.
self.assertEqual(False, feature_3 in new_strain.features)
self.assertEqual(False, feature_4 in new_strain.features)
self.assertEqual(1, len(new_strain.diff(strain))) # 'genome' changed
self.assertEqual(
'AAAAAAATAAAAAAAAAAAAAAAAACCCCCGCCCCCCGATGACCCCCCCCCCGGGGGGAGAGA',
str(new_genome.seq))
genome_fdiff = new_strain.components['genome'].fdiff(
strain.components['genome'])
self.assertEqual(set(genome.features), set(
genome_fdiff.removed)) # all features removed/changed
self.assertEqual(Diff(changed=['genome']), new_strain.diff(strain))
self.assertEqual(
{
Feature(new_genome, FeatureLocation(0, 25), type="a"),
Feature(new_genome, FeatureLocation(52, 56), type="g"),
Feature(new_genome, FeatureLocation(25, 50), type="c")
}, set(genome_fdiff.added))
self.assertEqual(
{('a', 'AAAAAAATAAAAAAAAAAAAAAAAA'),
('c', 'CCCCCGCCCCCCGATGACCCCCCCC'), ('g', 'GGGG')},
set((f.type, str(f.seq)) for f in genome_fdiff.added))
def test_quickstart_feature_inherit(self):
slogan = Component('CoPy is for DNA components',
features=[
SeqFeature(FeatureLocation(0, 4), type='name'),
SeqFeature(FeatureLocation(12, 15), id='DNA')
])
self.assertEqual('components',
str(slogan.features.add(FeatureLocation(16, 26)).seq))
self.assertEqual(['CoPy', 'DNA', 'components'],
[str(f.seq) for f in slogan.features])
new_slogan = slogan.mutate([DEL(2, 2), DEL(12, 4)])
self.assertEqual('Co is for components', str(new_slogan.seq))
self.assertEqual([
Feature(new_slogan, FeatureLocation(0, 2), type='name'),
Feature(new_slogan, FeatureLocation(10, 20))
], list(new_slogan.features))
self.assertEqual(['Co', 'components'],
[str(f.seq) for f in new_slogan.features])
def test_inherited_search(self):
letters = Component('AABBDDEE',
features=[
SeqFeature(FeatureLocation(0, 1),
type='vowel'),
SeqFeature(FeatureLocation(2, 5),
type='consonant'),
SeqFeature(FeatureLocation(5, 6), type='vowel')
])
letters = letters.mutate([INS(4, 'CC')])
self.assertEqual('AABBCCDDEE', str(letters.seq))
self.assertEqual([
Feature(letters, FeatureLocation(0, 1), type='vowel'),
Feature(letters, FeatureLocation(7, 8), type='vowel')
], list(letters.features.find(type='vowel')))
self.assertEqual([],
list(
letters.features.find(type='consonant',
between_end=1)))
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_inherit_feature_delete(self):
orig = Component(
'TTACCCATT',
features=[SeqFeature(FeatureLocation(0, 1), type='tt')])
f = orig.features.add(FeatureLocation(3, 6), type='ccc')
self.assertEqual('CCC', str(f.seq))
mutated = orig.mutate([DEL(3, 3)])
self.assertEqual('TTAATT', str(mutated.seq))
self.assertEqual([Feature(mutated, FeatureLocation(0, 1), type='tt')],
list(mutated.features))