本文整理汇总了Python中puzzle.plugins.GeminiPlugin.add_case方法的典型用法代码示例。如果您正苦于以下问题：Python GeminiPlugin.add_case方法的具体用法？Python GeminiPlugin.add_case怎么用？Python GeminiPlugin.add_case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.add_case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_no_filters_sv
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import add_case [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2: 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 add_case [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3: 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 add_case [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4: 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 add_case [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5: 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 add_case [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6: test_variant
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import add_case [as 别名]
def test_variant(gemini_case_obj):
"""Test to get one variant"""
plugin = GeminiPlugin()
plugin.add_case(gemini_case_obj)
variant = plugin.variant(
case_id='643594',
variant_id=4
)
assert variant['CHROM'] == '6'
assert variant['POS'] == '32487163'
assert type(variant['genes']) == type([])示例7: 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 add_case [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8: test_filters_cadd
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import add_case [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9: test_filters_frequency
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import add_case [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示例10: test_filters_consequence
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import add_case [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11: test_filters_range
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import add_case [as 别名]
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示例12: test_add_transcripts
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import add_case [as 别名]
def test_add_transcripts(self, gemini_case_obj, variant):
adapter = GeminiPlugin()
adapter.add_case(gemini_case_obj)
adapter.db = gemini_case_obj.variant_source
gemini_variant = {'variant_id': 1}
adapter._add_transcripts(variant, gemini_variant)
transcripts = variant.transcripts
assert len(transcripts) == 2
first_transcript = transcripts[0]
assert first_transcript.transcript_id == 'ENST00000370383'
assert first_transcript.hgnc_symbol == 'EPHX4'
assert first_transcript.consequence == 'missense_variant'
assert first_transcript.ensembl_id == None
assert first_transcript.biotype == 'protein_coding'
assert first_transcript.sift == 'deleterious'
assert first_transcript.polyphen == 'probably_damaging'示例13: test_get_individuals
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import add_case [as 别名]
def test_get_individuals(gemini_case_obj):
adapter = GeminiPlugin()
adapter.add_case(gemini_case_obj)
ind_ids = [ind.ind_id for ind in adapter.individual_objs]
assert set(ind_ids) == set(['NA12877', 'NA12878', 'NA12882'])示例14: test_case_no_id
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import add_case [as 别名]
def test_case_no_id(gemini_case_obj):
adapter = GeminiPlugin()
adapter.add_case(gemini_case_obj)
case_id = '643594'
assert adapter.case().case_id == case_id示例15: test_get_individuals_one_ind
# 需要导入模块: from puzzle.plugins import GeminiPlugin [as 别名]
# 或者: from puzzle.plugins.GeminiPlugin import add_case [as 别名]
def test_get_individuals_one_ind(gemini_case_obj):
adapter = GeminiPlugin()
adapter.add_case(gemini_case_obj)
ind_ids = [ind.ind_id for ind in adapter.individuals('NA12877')]
assert set(ind_ids) == set(['NA12877'])