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_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_mutate_insert(self):
self.assertEqual('99012345',
str(Component('012345').mutate([INS(0, '99')]).seq))
self.assertEqual('09912345',
str(Component('012345').mutate([INS(1, '99')]).seq))
self.assertEqual(
'9912345',
str(Component('012345').mutate([INS(0, '99', replace=True)]).seq))
def test_mutate_replace(self):
self.assertEqual(
'01ttf2345',
str(Component('012345').mutate([Mutation(1, 1, '1ttf')]).seq))
self.assertEqual(
'0ott45',
str(Component('012345').mutate([Mutation(1, 3, 'ott')]).seq))
self.assertEqual('z12345',
str(Component('012345').mutate([SNP(0, 'z')]).seq))
def test_mutate_delete(self):
self.assertEqual('01234',
str(Component('012345').mutate([DEL(5)]).seq))
self.assertEqual('01235',
str(Component('012345').mutate([DEL(4)]).seq))
self.assertEqual('0123',
str(Component('012345').mutate([DEL(4, 2)]).seq))
self.assertEqual('2345',
str(Component('012345').mutate([DEL(0, 2)]).seq))
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))
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_inherit_features(self):
component = Component('ABCDEFGHIerrorJKLMNOPQRSTUVXYZ')
component.features.add(FeatureLocation(0, 3), id='abc') # fine
component.features.add(FeatureLocation(9, 14), id='error') # fine
component.features.add(FeatureLocation(6, 12), id='GHI..err')
component.features.add(FeatureLocation(11, 17), id='ror..JKL')
component.features.add(FeatureLocation(8, 15), id='I..error..J') # fine
component.features.add(FeatureLocation(29, 30), id='end') # fine
mutated = component.mutate([DEL(9, 5)])
self.assertEqual({'JKL', 'Z', 'ABC', 'GHI', 'IJ'}, set(str(f.seq) for f in mutated.features))
def test_lineage_simple(self):
generation1 = Component('Ax')
generation2 = generation1.mutate([INS(1, 'B')])
generation3 = generation2.mutate([INS(2, 'C')])
other = Component('a')
self.assertEqual('ABx', str(generation2.seq))
self.assertEqual(False, generation1.inherits_from(generation3))
self.assertEqual(True, generation3.inherits_from(generation1))
self.assertEqual(False, generation3.inherits_from(other))
self.assertEqual([generation2, generation1], list(generation3.get_lineage()))
def test_lineage_simple(self):
generation1 = Component('Ax')
generation2 = generation1.mutate([INS(1, 'B')])
generation3 = generation2.mutate([INS(2, 'C')])
other = Component('a')
self.assertEqual('ABx', str(generation2.seq))
self.assertEqual(False, generation1.inherits_from(generation3))
self.assertEqual(True, generation3.inherits_from(generation1))
self.assertEqual(False, generation3.inherits_from(other))
self.assertEqual([generation2, generation1],
list(generation3.get_lineage()))
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))
def test_inherit_features(self):
component = Component('ABCDEFGHIerrorJKLMNOPQRSTUVXYZ')
component.features.add(FeatureLocation(0, 3), id='abc') # fine
component.features.add(FeatureLocation(9, 14), id='error') # fine
component.features.add(FeatureLocation(6, 12), id='GHI..err')
component.features.add(FeatureLocation(11, 17), id='ror..JKL')
component.features.add(FeatureLocation(8, 15),
id='I..error..J') # fine
component.features.add(FeatureLocation(29, 30), id='end') # fine
mutated = component.mutate([DEL(9, 5)])
self.assertEqual({'JKL', 'Z', 'ABC', 'GHI', 'IJ'},
set(str(f.seq) for f in mutated.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_mutate_1(self):
component = Component('ABCDEFGHIJKLMNOPQRSTUVWXYZ')
# . . . . . .
mutated = component.mutate( # 01234567 8901234567890 12345
[SNP(3, 'd'), # ABCdEFGH IJKLMNOPQRSTU VWXYZ
DEL(1), # A-CdEFGH IJKLMNOPQRSTU VWXYZ
INS(21, 'xx'), # A-CdEFGH IJKLMNOPQRSTUxxVWXYZ
Mutation(10, 9, 'oops'), # A-CdEFGH IJoops-----TUxxVWXYZ
SUB(4, 'ef'), # A-CdefGH IJoops-----TUxxVWXYZ
Mutation(7, 1, 'Hh')], # A-CdefGHhIJoops-----TUxxVWXYZ
strict=False) # 0 1234567890123 457890123
# . . . . .
self.assertEqual('ACdefGHhIJoopsTUxxVWXYZ', str(mutated.seq))
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_mutate_1(self):
component = Component('ABCDEFGHIJKLMNOPQRSTUVWXYZ')
# . . . . . .
mutated = component.mutate( # 01234567 8901234567890 12345
[
SNP(3, 'd'), # ABCdEFGH IJKLMNOPQRSTU VWXYZ
DEL(1), # A-CdEFGH IJKLMNOPQRSTU VWXYZ
INS(21, 'xx'), # A-CdEFGH IJKLMNOPQRSTUxxVWXYZ
Mutation(10, 9, 'oops'), # A-CdEFGH IJoops-----TUxxVWXYZ
SUB(4, 'ef'), # A-CdefGH IJoops-----TUxxVWXYZ
Mutation(7, 1, 'Hh')
], # A-CdefGHhIJoops-----TUxxVWXYZ
strict=False) # 0 1234567890123 457890123
# . . . . .
self.assertEqual('ACdefGHhIJoopsTUxxVWXYZ', str(mutated.seq))
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_feature_non_strict_order(self):
"""
In non-strict mode, potentially ambiguous mutations are allowed where the order in which
the order in which the mutations are applied is significant.
"""
component = Component('12345', feature_class=Feature)
component.features.add(FeatureLocation(2, 4), type='34')
# |████| |████|
# 12|3 4|5 12|3 4|5
# 12|3xy4|5 12|3 -|5
# 12|3xy|-5 12|3 xy|5
mutated_1 = component.mutate([DEL(3), INS(3, 'xy')], strict=False)
self.assertEqual('3xy', str(list(mutated_1.features)[0].seq)) # 3 would also be acceptable.
self.assertEqual('123xy5', str(mutated_1.seq))
mutated_2 = component.mutate([INS(3, 'xy'), DEL(3)], strict=False)
self.assertEqual('3xy', str(list(mutated_2.features)[0].seq))
self.assertEqual('123xy5', str(mutated_2.seq))
def test_feature_non_strict_order(self):
"""
In non-strict mode, potentially ambiguous mutations are allowed where the order in which
the order in which the mutations are applied is significant.
"""
component = Component('12345', feature_class=Feature)
component.features.add(FeatureLocation(2, 4), type='34')
# |████| |████|
# 12|3 4|5 12|3 4|5
# 12|3xy4|5 12|3 -|5
# 12|3xy|-5 12|3 xy|5
mutated_1 = component.mutate([DEL(3), INS(3, 'xy')], strict=False)
self.assertEqual('3xy', str(list(
mutated_1.features)[0].seq)) # 3 would also be acceptable.
self.assertEqual('123xy5', str(mutated_1.seq))
mutated_2 = component.mutate([INS(3, 'xy'), DEL(3)], strict=False)
self.assertEqual('3xy', str(list(mutated_2.features)[0].seq))
self.assertEqual('123xy5', str(mutated_2.seq))
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_add_features(self):
component = Component('GAGAGAGATATAGAGAGA')
component.features.add(FeatureLocation(8, 12),
qualifiers={'name': 'tata'})
component.features.add(FeatureLocation(17, 18),
qualifiers={'name': 'end'})
component.features.add(FeatureLocation(0, 1),
qualifiers={'name': 'start'})
self.assertEqual(
['start', 'tata', 'end'],
[f.qualifiers.get('name') for f in component.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_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_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))
def test_export(self):
component = Component(Seq('TATAGAGACACA', alphabet=DNAAlphabet()),
id='Magic_Brick',
annotations={'accession': 'MB1'})
component.features.add(FeatureLocation(3, 7), type='-10_signal')
component.features.add(FeatureLocation(7, 9),
id='GA',
type='CDS',
qualifiers={'locus_id': 'b0001'})
# GenbankConverter.to_file(component, 'fixtures/MB_1.gb', 'Magic_Brick')
record = GenbankConverter.to_seq_record(component)
self.assertEqual(
open('tests/fixtures/MB_1.gb').read(), record.format('genbank'))