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_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([])
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_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_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([])
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_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_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_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_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_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
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'
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'
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'])
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
def test_case_wrong_id(gemini_case_obj):
adapter = GeminiPlugin()
adapter.add_case(gemini_case_obj)
case_id = 'hello'
assert adapter.case(case_id) == None
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'])
def test_case_objs(gemini_case_obj):
adapter = GeminiPlugin()
adapter.add_case(gemini_case_obj)
case_ids = [case.case_id for case in adapter.case_objs]
assert set(case_ids) == set(['643594'])