def test_insertion_followed_by_deletion(state):
state.change(Change(None, F('foo')))
assert state.changes == (Change(None, F('foo')), )
state.change(Change(F('foo'), None))
assert state.changes == ()
def test_change_that_cancels_out(state):
state.change(Change(F('a'), F('b')))
assert state.changes == (Change(F('a'), F('b')), )
state.change(Change(F('b'), F('a')))
assert state.changes == ()
def test_standalone_change_at_replaced_locus(state):
state.change(Change(F('a'), F('b')))
assert state.changes == (Change(F('a'), F('b')), )
state.change(Change(AtLocus(F('b'), F('a')), F('c')))
assert state.changes == (Change(F('a'), F('c')), )
def test_parse_fusion(parse):
assert [Change(after=Fusion(Feature('foo'), Feature('bar')))
] == parse('+foo:bar')
assert [
Change(before=Fusion(Feature('foo'), Feature('bar')),
after=Feature('foo'))
] == parse('foo:bar>foo')
def test_change_presence(state):
state.change(Present(F.parse('gene.foo(A)')))
assert state.changes == (Change(None, F.parse('gene.foo(A)')), )
state.change(Present(F.parse('gene.foo(B)')))
assert state.changes == (Change(None, F.parse('gene.foo(B)')), )
def test_replace_fusion():
assert Change(
before=Feature('a'), after=Fusion(
Feature('b'),
Feature('c'))) == (Feature('a') > Feature('b')**Feature('c'))
assert Change(
before=Fusion(Feature('a'), Feature('b')),
after=Feature('c')) == (Feature('a')**Feature('b') > Feature('c'))
def test_change_at_locus_when_before_is_at_locus(state):
state.change(Change(F('a') % F('a'), F('b')))
assert state.changes == (Change(F('a'), F('b')), )
state.change(Change(F('c') % F('c'), None))
assert state.changes == (
Change(F('a'), F('b')),
Change(F('c'), None),
)
def test_imply_locus_with_substitution():
assert chain('gene.A>promoter.X:gene.B', 'gene.C>promoter.X:gene.D',
'[email protected]>promoter.Y').changes() == (
Change(
Feature.parse('gene.C'),
Fusion(Feature.parse('promoter.X'),
Feature.parse('gene.D'))),
Change(
Feature.parse('gene.A'),
Fusion(Feature.parse('promoter.Y'),
Feature.parse('gene.B'))),
)
def test_parse_composite_annotation(parse):
assert [
Change(after=CompositeAnnotation(Feature('geneA'), Feature('geneB')))
] == parse('+{geneA, geneB}')
assert [
Change(before=CompositeAnnotation(Feature('geneA'), Feature('geneB')))
] == parse('-{geneA, geneB}')
assert [
Change(before=Feature('geneX'),
after=Fusion(
CompositeAnnotation(Feature('geneA'), Feature('geneB')),
Feature('geneX')))
] == parse('geneX>{geneA, geneB}:geneX')
def test_scenario_1c_disambiguate_site_using_repeat_site(state):
state.change(
Change(F.parse('gene.A'),
F.parse('promoter.X')**F.parse('gene.B')))
state.change(
Change(F.parse('gene.C'),
F.parse('promoter.X')**F.parse('gene.D')))
state.change(
Change(F.parse('gene.A'),
F.parse('promoter.Y')**F.parse('gene.B')))
assert state.changes == (Change(F.parse('gene.C'),
F.parse('promoter.X')**F.parse('gene.D')),
Change(F.parse('gene.A'),
F.parse('promoter.Y')**F.parse('gene.B')))
def to_gnomic(self):
accession = Target.to_gnomic(self)
pairs = [(m.id for m in pair) for pair in self.swap_pairs]
wt_feature = Feature(name=self.id, accession=accession, type='reaction',
variant=["cofactors=%s" % ",".join(pairs[0])])
feature = Feature(name=self.id, accession=accession, type='reaction',
variant=["cofactors=%s" % ",".join(pairs[1])])
return Change(before=wt_feature, after=feature)
def to_gnomic(self):
accession = Target.to_gnomic(self)
if self._value == 0:
old_feature = Feature(name=self.id, accession=accession, type=self.__gnomic_feature_type__)
new_feature = None
elif self.fold_change != 0:
old_feature = Feature(name=self.id, type=self.__gnomic_feature_type__,
variant=tuple(["value={}".format(self._reference_value)]))
new_feature = Feature(name=self.id, accession=accession, type=self.__gnomic_feature_type__,
variant=tuple(["value={}".format(self._value)]))
else:
raise RuntimeError("fold_change shouldn't be 0")
return Change(before=old_feature, after=new_feature)
def test_replacement_of_variants(state):
state.change(Change(F.parse('a(x)'), F('b')))
assert state.changes == (Change(F.parse('a(x)'), F('b')), )
state.change(Change(F.parse('a(y)'), F('b')))
assert state.changes == (
Change(F.parse('a(x)'), F('b')),
Change(F.parse('a(y)'), F('b')),
)
state.change(Change(F.parse('a(y)'), F('c')))
assert state.changes == (
Change(F.parse('a(x)'), F('b')),
Change(F.parse('a(y)'), F('c')),
)
def test_change_gnomic_format(gnomic_formatter):
assert gnomic_formatter.format_change(
Change(before=Feature('foo'))) == '-foo'
assert gnomic_formatter.format_change(
Change(after=Feature('foo'))) == '+foo'
assert gnomic_formatter.format_change(
Change(before=Feature('foo'), after=Feature('bar'))) == 'foo>bar'
assert gnomic_formatter.format_change(
Change(before=Feature('foo'), after=Feature('bar'),
multiple=True)) == 'foo>>bar'
assert gnomic_formatter.format_change(
Change(after=Plasmid('foo'))) == '(foo)'
assert gnomic_formatter.format_change(
Change(before=Feature('foo'),
after=Feature('foo', variant=['x']))) == 'foo(x)'
assert gnomic_formatter.format_change(
Change(before=Feature('foo', variant=['x']),
after=Feature('foo', variant=['y']))) == 'foo(y)'
assert gnomic_formatter.format_change(
Change(before=AtLocus(Feature('foo', variant=['x']), Feature('f')),
after=Feature('foo', variant=['y']))) == 'foo(x)@f>foo(y)'
def test_replacement_in_fusion_at_locus(state):
state.change(Change(F('x'), F('a')**F('b')))
state.change(Change(F('y'), F('a')**F('b')))
assert state.changes == (
Change(F('x'),
F('a')**F('b')),
Change(F('y'),
F('a')**F('b')),
)
state.change(Change(F('b') % F('y'), F('b')**F('c')))
assert state.changes == (
Change(F('x'),
F('a')**F('b')),
Change(F('y'),
F('a')**F('b')**F('c')),
)
def change(self, change):
# XXX consider not simplifying (foo@foo>... and -foo@foo) if there is a logical use
# simplify change at locus where annotation and locus are the same (e.g. foo@foo>... or -foo@foo)
if change.before and isinstance(
change.before,
AtLocus) and change.before.annotation == change.before.locus:
change = Change(change.before.annotation,
change.after,
multiple=change.multiple)
if change.before is None:
# e.g. +gene.A
self.insert(change.after, multiple=change.multiple)
elif change.after is None:
# e.g. -gene.A
self.remove(change.before, multiple=change.multiple)
else:
# e.g. gene.A>gene.B
assert change.before and change.after
self.replace(change.before, change.after, multiple=change.multiple)
def test_scenario_2_change_at_unknown_locus(state):
state.change(
Change(
F.parse('promoter.A') % F.parse('gene.foo'),
F.parse('promoter.B')))
assert state.changes == (Change(
F.parse('promoter.A') % F.parse('gene.foo'), F.parse('promoter.B')), )
state.change(Change(None, F.parse('gene.foo')))
assert state.changes == (
Change(
F.parse('promoter.A') % F.parse('gene.foo'),
F.parse('promoter.B')),
Change(None, F.parse('gene.foo')),
)
state.change(
Change(
F.parse('promoter.B') % F.parse('gene.foo'),
F.parse('promoter.A')))
assert state.changes == (Change(None, F.parse('gene.foo')), )
def INSERTION(self, ast):
return Change(after=ast.after)
def to_gnomic(self):
accession = Target.to_gnomic(self)
feature = Feature(name=self.id, accession=accession)
return Change(before=feature)
def to_gnomic(self):
accession = Target.to_gnomic(self)
feature = Feature(accession=accession, type='reaction', name=self.id)
return Change(after=feature)
def test_replace_feature_at_locus():
assert Change(
before=AtLocus(Feature('a'), Feature('site')),
after=Feature('b')) == (Feature('a') % Feature('site') > Feature('b'))
def test_remove_feature_at_locus():
assert Change(before=AtLocus(Feature('foo'), Feature(
'site'))) == -Feature('foo') % Feature('site')
with pytest.raises(ValueError):
-Feature('foo') % Feature('a') % Feature('b')
def test_insert_fusion():
assert Change(after=Fusion(Feature('a'), Feature(
'b'))) == +Feature('a')**Feature('b')
def PHENE(self, ast):
return Change(after=self.FEATURE(ast), multiple=True)
def CHANGE(self, ast):
if isinstance(ast, Plasmid):
return Change(after=ast)
return ast
def DELETION(self, ast):
return Change(before=ast.before)
def REPLACEMENT(self, ast):
return Change(before=ast.before,
after=ast.after,
multiple=ast.op == '>>')
def test_remove_feature():
assert Change(before=Feature('foo')) == -Feature('foo')
def test_insert_feature():
assert Change(after=Feature('foo')) == +Feature('foo')
def test_remove_fusion():
assert Change(before=Fusion(Feature('a'), Feature(
'b'))) == -Feature('a')**Feature('b')