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_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])])
