def test_individual(case_obj):
adapter=VcfPlugin()
adapter.add_case(case_obj)
ind_id = "ADM1059A1"
ind_obj = adapter.individual(ind_id)
assert ind_obj.ind_id == ind_id
def test_filters_no_filter(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {}
result = plugin.variants(case_id, filters=filters, count=1000)
assert result.nr_of_variants == 108
def test_filters_no_filter(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {}
result = plugin.variants(case_id, filters=filters, count=1000)
assert result.nr_of_variants == 108
def test_variant(case_obj):
vcf_plugin = VcfPlugin()
vcf_plugin.add_case(case_obj)
variant = vcf_plugin.variant(case_obj.case_id, 'X_155239821_G_A')
assert variant['CHROM'] == 'X'
assert int(variant['POS']) == 155239821
# get 10th variant
variant = vcf_plugin.variant(case_obj.case_id, '3_124998098_C_A')
assert variant['index'] == 10
def test_variant(case_obj):
vcf_plugin = VcfPlugin()
vcf_plugin.add_case(case_obj)
variant = vcf_plugin.variant(case_obj.case_id, 'X_155239821_G_A')
assert variant['CHROM'] == 'X'
assert int(variant['POS']) == 155239821
# get 10th variant
variant = vcf_plugin.variant(case_obj.case_id, '3_124998098_C_A')
assert variant['index'] == 10
def test_filters_frequency(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {'frequency':'0.001'}
result = plugin.variants(case_id, filters=filters, count=1000)
variants = result.variants
nr_of_variants = result.nr_of_variants
for variant_obj in variants:
assert variant_obj.max_freq <= 0.001
assert nr_of_variants == 88
def test_filters_frequency(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {'frequency':'0.001'}
result = plugin.variants(case_id, filters=filters, count=1000)
variants = result.variants
nr_of_variants = result.nr_of_variants
for variant_obj in variants:
assert variant_obj.max_freq <= 0.001
assert nr_of_variants == 73
def test_filters_consequence(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {'consequence':['frameshift_variant']}
result = plugin.variants(case_id, filters=filters, count=1000)
variants = result.variants
nr_of_variants = result.nr_of_variants
for variant_obj in variants:
assert 'frameshift_variant' in variant_obj.consequences
assert nr_of_variants == 4
def test_filters_gene_ids(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {'gene_ids':['POF1B']}
result = plugin.variants(case_id, filters=filters, count=1000)
variants = result.variants
nr_of_variants = result.nr_of_variants
for variant_obj in variants:
assert 'POF1B' in variant_obj.gene_symbols
assert nr_of_variants == 1
def test_filters_impact_severities_high(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {'impact_severities':['HIGH']}
result = plugin.variants(case_id, filters=filters, count=1000)
variants = result.variants
nr_of_variants = result.nr_of_variants
for variant_obj in variants:
assert variant_obj.impact_severity == 'HIGH'
assert nr_of_variants == 7
def test_filters_cadd(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {'cadd':'20'}
result = plugin.variants(case_id, filters=filters, count=1000)
variants = result.variants
nr_of_variants = result.nr_of_variants
for variant_obj in variants:
variant_obj.cadd_score >= 20
assert nr_of_variants == 50
def test_filters_consequence(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {'consequence':['frameshift_variant']}
result = plugin.variants(case_id, filters=filters, count=1000)
variants = result.variants
nr_of_variants = result.nr_of_variants
for variant_obj in variants:
assert 'frameshift_variant' in variant_obj.consequences
assert nr_of_variants == 4
def test_filters_impact_severities_high(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {'impact_severities':['HIGH']}
result = plugin.variants(case_id, filters=filters, count=1000)
variants = result.variants
nr_of_variants = result.nr_of_variants
for variant_obj in variants:
assert variant_obj.impact_severity == 'HIGH'
assert nr_of_variants == 7
def test_filters_gene_ids(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {'gene_ids':['POF1B']}
result = plugin.variants(case_id, filters=filters, count=1000)
variants = result.variants
nr_of_variants = result.nr_of_variants
for variant_obj in variants:
assert 'POF1B' in variant_obj.gene_symbols
assert nr_of_variants == 1
def test_filters_cadd(self, case_obj):
plugin = VcfPlugin()
plugin.add_case(case_obj)
case_id = case_obj.case_id
filters = {'cadd':'20'}
result = plugin.variants(case_id, filters=filters, count=1000)
variants = result.variants
nr_of_variants = result.nr_of_variants
for variant_obj in variants:
variant_obj.cadd_score >= 20
assert nr_of_variants == 50
def test_variants_case(case_obj):
vcf_plugin = VcfPlugin()
vcf_plugin.add_case(case_obj)
#case_id is 'hapmap.vcf' since no ped file is given
result = vcf_plugin.variants(case_id=case_obj.case_id)
variants = result.variants
variant = variants[0]
assert variant['CHROM'] == 'X'
assert int(variant['POS']) == 84563218
assert variant['index'] == 1
variant = variants[1]
assert variant['CHROM'] == '2'
assert int(variant['POS']) == 233349186
assert variant['index'] == 2
def test_variants_case(case_obj):
vcf_plugin = VcfPlugin()
vcf_plugin.add_case(case_obj)
#case_id is 'hapmap.vcf' since no ped file is given
result = vcf_plugin.variants(case_id=case_obj.case_id)
variants = result.variants
variant = variants[0]
assert variant['CHROM'] == 'X'
assert int(variant['POS']) == 84563218
assert variant['index'] == 1
variant = variants[1]
assert variant['CHROM'] == '2'
assert int(variant['POS']) == 233349186
assert variant['index'] == 2
def select_plugin(self, case_obj):
"""Select and initialize the correct plugin for the case."""
if case_obj.variant_mode == "vcf":
logger.debug("Using vcf plugin")
plugin = VcfPlugin(case_obj.variant_type)
elif case_obj.variant_mode == "gemini":
logger.debug("Using gemini plugin")
plugin = GeminiPlugin(case_obj.variant_type)
# Add case to plugin
plugin.add_case(case_obj)
self.variant_type = case_obj.variant_type
case_id = case_obj.case_id
return plugin, case_id
def select_plugin(self, case_obj):
"""Select and initialize the correct plugin for the case."""
if case_obj.variant_mode == 'vcf':
logger.debug("Using vcf plugin")
plugin = VcfPlugin(case_obj.variant_type)
elif case_obj.variant_mode == 'gemini':
logger.debug("Using gemini plugin")
plugin = GeminiPlugin(case_obj.variant_type)
#Add case to plugin
plugin.add_case(case_obj)
self.variant_type = case_obj.variant_type
case_id = case_obj.case_id
return plugin, case_id
def test_filters_range(self, case_obj, indexed_vcf_file):
plugin = VcfPlugin()
case_obj.variant_source = indexed_vcf_file
case_obj.compressed = True
case_obj.tabix_index = True
plugin.add_case(case_obj)
case_id = case_obj.case_id
start = 1771120
end = 1771130
filters = {'range':{'chromosome':'1', 'start':start, 'end':end}}
result = plugin.variants(case_id, 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, case_obj, indexed_vcf_file):
plugin = VcfPlugin()
case_obj.variant_source = indexed_vcf_file
case_obj.compressed = True
case_obj.tabix_index = True
plugin.add_case(case_obj)
case_id = case_obj.case_id
start = 1771120
end = 1771130
filters = {'range':{'chromosome':'1', 'start':start, 'end':end}}
result = plugin.variants(case_id, 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_case(case_obj):
adapter=VcfPlugin()
adapter.add_case(case_obj)
assert len(adapter.individual_objs) == 3
case_obj = adapter.case_objs[0]
assert case_obj.name == "636808"
def test_case(case_obj):
adapter=VcfPlugin()
adapter.add_case(case_obj)
case_id = "636808"
case_obj = adapter.case(case_id)
assert case_obj.case_id == case_id
def test_individuals(case_obj):
adapter=VcfPlugin()
adapter.add_case(case_obj)
individuals = [ind for ind in adapter.individuals()]
assert len(individuals) == 3
def test_cases(case_obj):
adapter=VcfPlugin()
adapter.add_case(case_obj)
case_id = "636808"
case_obj = adapter.cases()[0]
assert case_obj.name == "636808"
