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'
