def test_filters_cadd(self, gemini_path): adapter = GeminiPlugin(db=gemini_path) filters = {'cadd':'20'} variants = [] for variant in adapter.variants('643594', filters=filters): variants.append(variant) assert len(variants) == 4
def test_filters_gene_ids(self, gemini_path): adapter = GeminiPlugin(db=gemini_path) filters = {'gene_ids':['HLA-DRB5']} variants = [] for variant in adapter.variants('643594', filters=filters): variants.append(variant) assert len(variants) == 5
def test_filters_consequence(self, gemini_path): adapter = GeminiPlugin(db=gemini_path) filters = {'consequence':['stop_gained']} variants = [] for variant in adapter.variants('643594', filters=filters): variants.append(variant) assert len(variants) == 2
def test_filters_impact_severities(self, gemini_path): adapter = GeminiPlugin(db=gemini_path) filters = {'impact_severities':['HIGH']} variants = [] for variant in adapter.variants('643594', filters=filters): variants.append(variant) assert len(variants) == 2
def test_filters_frequency(self, gemini_path): adapter = GeminiPlugin(db=gemini_path) filters = {'frequency':'0.01'} variants = [] for variant in adapter.variants('643594', filters=filters): variants.append(variant) assert len(variants) == 13
def test_get_all_variants(gemini_path): """Test to get some variants from the gemini adapter""" adapter = GeminiPlugin(db=gemini_path) variants = [] for variant in adapter.variants('643594'): variants.append(variant) assert len(variants) == 14
def test_no_filters_sv(self, gemini_sv_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_sv_case_obj) filters = {} result = plugin.variants('hapmap', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants assert nr_of_variants == 513
def test_filters_no_filters(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants assert nr_of_variants == 14
def test_no_filters_sv(self, gemini_sv_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_sv_case_obj) filters = {} result = plugin.variants('hapmap', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants assert nr_of_variants == 513
def test_filters_no_filters(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants assert nr_of_variants == 14
def test_get_all_variants(gemini_case_obj): """Test to get some variants from the gemini adapter""" plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants assert nr_of_variants == 14
def test_get_all_variants(gemini_case_obj): """Test to get some variants from the gemini adapter""" plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants assert nr_of_variants == 14
def test_filters_impact_severities_medium(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {'impact_severities':['MEDIUM']} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert variant_obj.impact_severity == 'MEDIUM' assert nr_of_variants == 10
def test_filters_impact_severities_medium(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {'impact_severities': ['MEDIUM']} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert variant_obj.impact_severity == 'MEDIUM' assert nr_of_variants == 10
def test_filters_gene_ids(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {'gene_ids': ['HLA-DRB5']} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert 'HLA-DRB5' in variant_obj.gene_symbols assert nr_of_variants == 5
def test_filters_frequency(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {'frequency':'0.01'} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert variant_obj.max_freq < 0.01 assert nr_of_variants == 13
def test_filters_consequence(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {'consequence': ['stop_gained']} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert 'stop_gained' in variant_obj.consequences assert nr_of_variants == 2
def test_filters_sv_len(self, gemini_sv_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_sv_case_obj) filters = {'sv_len':'800'} result = plugin.variants('hapmap', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert variant_obj.sv_len >= 800 assert nr_of_variants == 176
def test_filters_gene_ids(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {'gene_ids':['HLA-DRB5']} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert 'HLA-DRB5' in variant_obj.gene_symbols assert nr_of_variants == 5
def test_filters_cadd(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {'cadd':'20'} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert variant_obj.cadd_score > 20 assert nr_of_variants == 4
def test_filters_frequency(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {'frequency': '0.01'} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert variant_obj.max_freq < 0.01 assert nr_of_variants == 13
def test_filters_sv_len(self, gemini_sv_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_sv_case_obj) filters = {'sv_len': '800'} result = plugin.variants('hapmap', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert variant_obj.sv_len >= 800 assert nr_of_variants == 176
def test_filters_consequence(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {'consequence':['stop_gained']} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert 'stop_gained' in variant_obj.consequences assert nr_of_variants == 2
def test_filters_cadd(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) filters = {'cadd': '20'} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert variant_obj.cadd_score > 20 assert nr_of_variants == 4
def test_filters_range(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) start = 92498060 end = 92498100 filters = {'range': {'chromosome': 'chr1', 'start': start, 'end':end}} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert variant_obj.start >= start assert variant_obj.stop <= end assert nr_of_variants == 1
def test_filters_range(self, gemini_case_obj): plugin = GeminiPlugin() plugin.add_case(gemini_case_obj) start = 92498060 end = 92498100 filters = {'range': {'chromosome': 'chr1', 'start': start, 'end': end}} result = plugin.variants('643594', filters=filters, count=1000) variants = result.variants nr_of_variants = result.nr_of_variants for variant_obj in variants: assert variant_obj.start >= start assert variant_obj.stop <= end assert nr_of_variants == 1
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'