class TestGeminiAdapter(object):
"""Setup and test a gemini adapter"""
def setup(self):
"""docstring for setup"""
self.adapter = GeminiPlugin(GEMINI_DB)
def test_gemini_individuals(self):
"""docstring for test_gemini_individuals"""
ind_ids = set([individual['ind_id']
for individual in self.adapter.individuals])
assert ind_ids == set(['NA12877', 'NA12878', 'NA12882'])
def test_gemini_cases(self):
"""docstring for test_gemini_individuals"""
cases = set([case['name']
for case in self.adapter.cases()])
assert cases == set(['643594'])
def test_get_variants(self):
"""Test to get some variants from the gemini adapter"""
variants = []
for variant in self.adapter.variants('643594', count=5):
variants.append(variant)
assert len(variants) == 5
def test_get_variant(self):
"""Test to get one variant"""
variant = self.adapter.variant(
case_id='643594',
variant_id=4
)
assert variant['CHROM'] == '6'
assert variant['POS'] == '32487163'
def test_cases(gemini_path):
adapter = GeminiPlugin(db=gemini_path)
case_ids = [case.case_id for case in adapter.cases()]
assert set(case_ids) == set(['643594'])
def test_cases(gemini_case_obj):
adapter = GeminiPlugin()
adapter.add_case(gemini_case_obj)
case_ids = [case.case_id for case in adapter.cases()]
assert set(case_ids) == set(['643594'])
