本文整理汇总了Python中puzzle.plugins.GeminiPlugin.variants方法的典型用法代码示例。如果您正苦于以下问题：Python GeminiPlugin.variants方法的具体用法？Python GeminiPlugin.variants怎么用？Python GeminiPlugin.variants使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类puzzle.plugins.GeminiPlugin的用法示例。
在下文中一共展示了GeminiPlugin.variants方法的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_filters_impact_severities
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例2: test_filters_cadd
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例3: test_filters_gene_ids
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例4: test_filters_consequence
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例5: test_filters_frequency
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例6: test_get_all_variants
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例7: test_no_filters_sv
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例8: test_filters_no_filters
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例9: test_get_all_variants
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例10: test_filters_impact_severities_medium
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例11: test_filters_cadd
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例12: test_filters_gene_ids
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例13: test_filters_consequence
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例14: test_filters_sv_len
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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示例15: test_filters_frequency
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import variants [as 别名]
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