def test_annotate_variants(self):
"""
Annotate a file with observation frequencies.
We first import a subset of the observations with coverage.
"""
with self.fixture.data(AnnotationData, CoverageData, DataSourceData, VariationData) as data:
coverage = Coverage.query.get(
data.CoverageData.exome_subset_coverage.id)
result = tasks.import_coverage.delay(coverage.id)
assert coverage.task_done
variation = Variation.query.get(
data.VariationData.exome_subset_variation.id)
result = tasks.import_variation.delay(variation.id)
assert variation.task_done
variation.sample.active = True
annotation = Annotation.query.get(data.AnnotationData.exome_annotation.id)
query = Query('GLOBAL', expressions.parse('*'))
db.session.add(query)
annotation.queries = [query]
db.session.commit()
data_source = DataSource.query.get(
data.DataSourceData.exome_variation.id)
annotated_file = StringIO.StringIO()
with data_source.data() as data:
checksum, records = utils.digest(data)
with data_source.data() as data:
tasks.annotate_variants(data, annotated_file,
original_filetype=data_source.filetype,
annotated_filetype='vcf',
original_records=records,
queries=[query])
lines = annotated_file.getvalue().split('\n')
reader = vcf.Reader(lines)
assert_equal([(record.INFO['GLOBAL_VN'], record.INFO['GLOBAL_VF']) for record in reader],
[([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([0], [0.0]),
([0], [0.0]),
([0], [0.0]),
([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([1, 1], [1.0, 0.0]),
([0], [0.0]),
([1], [0.0]),
([1], [1.0]),
([1], [1.0])])
def test_expression(string):
expression = expressions.parse(string)
switched = expression.accept(Switcher())
assert_equal(compose(expression)
.replace('and', '%OLDAND%')
.replace('or', 'and')
.replace('%OLDAND%', 'or'),
compose(switched))
def test_write_annotation(self):
"""
Annotate a variants file.
We first import a subset of the observations with coverage.
"""
with self.fixture.data(AnnotationData, CoverageData, VariationData) as data:
coverage = Coverage.query.get(
data.CoverageData.exome_subset_coverage.id)
result = tasks.import_coverage.delay(coverage.id)
assert coverage.task_done
variation = Variation.query.get(
data.VariationData.exome_subset_variation.id)
result = tasks.import_variation.delay(variation.id)
assert variation.task_done
variation.sample.active = True
annotation = Annotation.query.get(data.AnnotationData.exome_annotation.id)
query = Query('GLOBAL', expressions.parse('*'))
db.session.add(query)
annotation.queries = [query]
db.session.commit()
result = tasks.write_annotation.delay(annotation.id)
assert_equal(result.state, 'SUCCESS')
assert annotation.task_done
with annotation.annotated_data_source.data() as data:
reader = vcf.Reader(data)
assert_equal([(record.INFO['GLOBAL_VN'], record.INFO['GLOBAL_VF']) for record in reader],
[([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([0], [0.0]),
([0], [0.0]),
([0], [0.0]),
([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([1, 1], [1.0, 0.0]),
([0], [0.0]),
([1], [0.0]),
([1], [1.0]),
([1], [1.0])])
def test_annotate_variants_multi_one_sample_one_sample(self):
"""
Annotate a file with observation frequencies against multiple samples
querying one and querying one.
We first import two subsets of the observations with coverage.
"""
with self.fixture.data(AnnotationData, CoverageData, DataSourceData, VariationData) as data:
coverage = Coverage.query.get(
data.CoverageData.exome_subset_coverage.id)
result = tasks.import_coverage.delay(coverage.id)
assert coverage.task_done
variation = Variation.query.get(
data.VariationData.exome_subset_variation.id)
result = tasks.import_variation.delay(variation.id)
assert variation.task_done
sample_a = variation.sample
coverage = Coverage.query.get(
data.CoverageData.exome_subsubset_coverage.id)
result = tasks.import_coverage.delay(coverage.id)
assert coverage.task_done
variation = Variation.query.get(
data.VariationData.exome_subsubset_variation.id)
result = tasks.import_variation.delay(variation.id)
assert variation.task_done
sample_b = variation.sample
sample_a.active = True
sample_b.active = True
annotation = Annotation.query.get(data.AnnotationData.exome_annotation.id)
query_a = Query('QA', expressions.parse('sample:%i' %
data.SampleData.exome_subset_sample.id))
db.session.add(query_a)
query_b = Query('QB', expressions.parse('sample:%i' %
data.SampleData.exome_subsubset_sample.id))
db.session.add(query_b)
annotation.queries = [query_a, query_b]
db.session.commit()
data_source = DataSource.query.get(
data.DataSourceData.exome_variation.id)
annotated_file = StringIO.StringIO()
with data_source.data() as data:
checksum, records = utils.digest(data)
with data_source.data() as data:
tasks.annotate_variants(data, annotated_file,
original_filetype=data_source.filetype,
annotated_filetype='vcf',
original_records=records,
queries=[query_a, query_b])
lines = annotated_file.getvalue().split('\n')
reader = vcf.Reader(lines)
assert_equal([(record.INFO['QA_VN'], record.INFO['QA_VF']) for record in reader],
[([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([0], [0.0]),
([0], [0.0]),
([0], [0.0]),
([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([1], [1.0]),
([1, 1], [1.0, 0.0]),
([0], [0.0]),
([1], [0.0]),
([1], [1.0]),
([1], [1.0])])
reader = vcf.Reader(lines)
assert_equal([(record.INFO['QB_VN'], record.INFO['QB_VF']) for record in reader],
[([1], [1.0]),
([1], [0.0]),
([1], [1.0]),
([0], [0.0]),
([0], [0.0]),
([0], [0.0]),
([1], [1.0]),
([0], [0.0]),
([1], [1.0]),
([1], [0.0]),
([1], [1.0]),
([1, 1], [1.0, 0.0]),
([0], [0.0]),
([1], [0.0]),
([1], [0.0]),
([1], [0.0])])
def test_expressions(string_left, string_right):
left = expressions.parse(string_left)
right = expressions.parse(string_right)
expression = expressions.make_conjunction(left, right)
assert_equal(compose(expression),
'(%s) and %s' % (string_left, string_right))
def test_expression(string, expected):
expression = expressions.parse(string)
only_short_values = expressions.test_clauses(expression, short_value)
assert_equal(only_short_values, expected)
def test_expression(string, expected):
expression = expressions.parse(string)
updated = expressions.update_clause_values(expression, add_one)
assert_equal(compose(updated), expected)
def test_expression(string, expected):
expression = expressions.parse(string)
filter_criterion = expressions.build_query_criterion(expression, build_clause)
clause = filter_criterion.compile(dialect=postgresql.dialect(),
compile_kwargs={'literal_binds': True})
assert_equal(clause.string.replace('\n', ''), expected)
def test_expression(expression, expected):
ast = expressions.parse(expression)
is_clause = ast.accept(ClauseTester())
assert_equal(is_clause, expected)
def test_expression(string):
expression = expressions.parse(string)
pretty_printed = expressions.pretty_print(expression)
assert_equal(compose(expression), pretty_printed)
def test_expression(string):
expression = expressions.parse(string)
identity = expressions.deep_copy(expression)
assert_equal(compose(expression), compose(identity))
def test_expression(string):
with assert_raises(SyntaxError):
expressions.parse(string)
def test_expression(string, composed):
assert_equal(compose(expressions.parse(string)), composed)