def test_add_thousand_g(self, variant):
adapter = GeminiPlugin()
gemini_variant = {'aaf_1kg_all':0.01}
adapter._add_thousand_g(variant, gemini_variant)
assert variant.thousand_g == 0.01
assert len(variant.frequencies) == 1
def test_is_variant(case_obj):
adapter = GeminiPlugin()
genotypes = ['G/A', 'G/A', 'G/G', 'G/G', './.']
ind_objs = [
Individual(ind_id=0, ind_index=0),
Individual(ind_id=1, ind_index=1),
]
#Mock a gemini variant
gemini_variant = {
'gts':genotypes,
'alt':'A'
}
assert adapter._is_variant(gemini_variant, ind_objs)
#Check with individuals that are hom ref
ind_objs = [
Individual(ind_id=0, ind_index=2),
Individual(ind_id=1, ind_index=3),
]
assert not adapter._is_variant(gemini_variant, ind_objs)
#Check with individual that has no call
ind_objs = [
Individual(ind_id=0, ind_index=4),
]
assert not adapter._is_variant(gemini_variant, ind_objs)
def test_add_exac(self, variant):
adapter = GeminiPlugin()
gemini_variant = {'aaf_exac_all': 0.01}
adapter._add_exac(variant, gemini_variant)
assert variant.thousand_g == None
assert len(variant.frequencies) == 1
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_add_gmaf_no_frequency(self, variant):
adapter = GeminiPlugin()
gemini_variant = {'max_aaf_all': None}
adapter._add_gmaf(variant, gemini_variant)
assert len(variant.frequencies) == 0
assert variant.max_freq == None
def test_add_genotypes(self, variant):
adapter = GeminiPlugin()
gemini_variant = {
'gts': ['G/A', 'G/A', './.', './.', './.'],
'gt_depths': [17, 19, -1, -1, -1],
'gt_ref_depths': [10, 13, -1, -1, -1],
'gt_alt_depths': [7, 6, -1, -1, -1],
'gt_quals': [99, 99, -1, -1, -1],
}
ind = DotDict()
ind.ind_index = 0
ind.ind_id = '1'
ind.case_id = 'Case_1'
ind.phenotype = 2
ind_objs = [ind]
adapter._add_genotypes(variant, gemini_variant, ind_objs)
genotype = variant.individuals[0]
assert genotype.sample_id == ind.ind_id
assert genotype.sample_id == ind.ind_id
assert genotype.genotype == 'G/A'
assert genotype.case_id == ind.case_id
assert genotype.phenotype == ind.phenotype
assert genotype.ref_depth == 10
assert genotype.alt_depth == 7
assert genotype.depth == 17
assert genotype.genotype_quality == 99
def test_add_genotypes(self, variant):
adapter = GeminiPlugin()
gemini_variant = {
'gts': ['G/A', 'G/A', './.', './.', './.'],
'gt_depths': [17, 19, -1, -1, -1],
'gt_ref_depths': [10, 13, -1, -1, -1],
'gt_alt_depths': [7, 6, -1, -1, -1],
'gt_quals': [99, 99, -1, -1, -1],
}
ind = DotDict()
ind.ind_index = 0
ind.ind_id = '1'
ind.phenotype = 2
ind_objs = [ind]
adapter._add_genotypes(variant, gemini_variant, 'dummy', ind_objs)
genotype = variant.individuals[0]
assert genotype.sample_id == ind.ind_id
assert genotype.sample_id == ind.ind_id
assert genotype.genotype == 'G/A'
assert genotype.case_id == 'dummy'
assert genotype.phenotype == ind.phenotype
assert genotype.ref_depth == 10
assert genotype.alt_depth == 7
assert genotype.depth == 17
assert genotype.genotype_quality == 99
def test_is_variant(gemini_case_obj):
plugin = GeminiPlugin()
genotypes = ['G/A', 'G/A', 'G/G', 'G/G', './.']
gt_types = [1, 1, 0, 0, 2]
ind_objs = [
Individual(ind_id=0, ind_index=0),
Individual(ind_id=1, ind_index=1),
]
#Mock a gemini variant
gemini_variant = {'gts': genotypes, 'gt_types': gt_types, 'alt': 'A'}
assert plugin._is_variant(gemini_variant, ind_objs)
#Check with individuals that are hom ref
ind_objs = [
Individual(ind_id=0, ind_index=2),
Individual(ind_id=1, ind_index=3),
]
assert not plugin._is_variant(gemini_variant, ind_objs)
#Check with individual that has no call
ind_objs = [
Individual(ind_id=0, ind_index=4),
]
assert not plugin._is_variant(gemini_variant, ind_objs)
def test_add_gmaf_no_frequency(self, variant):
adapter = GeminiPlugin()
gemini_variant = {'max_aaf_all':None}
adapter._add_gmaf(variant, gemini_variant)
assert len(variant.frequencies) == 0
assert variant.max_freq == None
def test_add_thousand_g(self, variant):
adapter = GeminiPlugin()
gemini_variant = {'aaf_1kg_all': 0.01}
adapter._add_thousand_g(variant, gemini_variant)
assert variant.thousand_g == 0.01
assert len(variant.frequencies) == 1
def test_add_exac(self, variant):
adapter = GeminiPlugin()
gemini_variant = {'aaf_exac_all':0.01}
adapter._add_exac(variant, gemini_variant)
assert variant.thousand_g == None
assert len(variant.frequencies) == 1
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_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_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_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_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_build_gemini_query():
plugin = GeminiPlugin()
query = "SELECT * from variants"
extra_info = "max_aaf_all < 0.01"
new_query = plugin.build_gemini_query(query, extra_info)
assert new_query == "SELECT * from variants WHERE max_aaf_all < 0.01"
extra_info = "cadd_score > 10"
new_query = plugin.build_gemini_query(new_query, extra_info)
assert new_query == "SELECT * from variants WHERE max_aaf_all < 0.01 AND cadd_score > 10"
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_build_gemini_query():
adapter = GeminiPlugin()
query = "SELECT * from variants"
extra_info = "max_aaf_all < 0.01"
new_query = adapter.build_gemini_query(query, extra_info)
assert new_query == "SELECT * from variants WHERE max_aaf_all < 0.01"
extra_info = "cadd_score > 10"
new_query = adapter.build_gemini_query(new_query, extra_info)
assert new_query == "SELECT * from variants WHERE max_aaf_all < 0.01 AND cadd_score > 10"
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_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_variant(gemini_path):
"""Test to get one variant"""
adapter = GeminiPlugin(db=gemini_path)
variant = adapter.variant(
case_id='643594',
variant_id=4
)
assert variant['CHROM'] == '6'
assert variant['POS'] == '32487163'
assert type(variant['genes']) == type([])
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_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_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_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_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_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_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_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_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_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
def test_get_transcripts(gemini_path):
adapter = GeminiPlugin(db=gemini_path)
gemini_variant = {'variant_id': 1}
transcripts = []
for transcript in adapter._get_transcripts(gemini_variant):
transcripts.append(transcript)
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_check_gemini_db(gemini_path, vcf_file):
adapter = GeminiPlugin()
adapter.db = gemini_path
assert adapter.test_gemini_db()
adapter.db = vcf_file
with pytest.raises(DatabaseError):
adapter.test_gemini_db()
def test_setup_no_db():
"""Test to initialize a gemini database without any file"""
adapter = GeminiPlugin()
assert adapter.db == None
assert adapter.variant_type == 'snv'
assert adapter.filters.can_filter_gene == True
assert adapter.filters.can_filter_inheritance == False
def test_get_genotypes(gemini_variant):
adapter = GeminiPlugin()
ind = DotDict()
ind.ind_index = 0
ind.ind_id = '1'
ind.case_id = 'Case_1'
ind.phenotype = 2
ind_objs = [ind]
individual = adapter._get_genotypes(gemini_variant, ind_objs)[0]
assert individual.sample_id == ind.ind_id
assert individual.sample_id == ind.ind_id
assert individual.genotype == 'G/A'
assert individual.case_id == ind.case_id
assert individual.phenotype == ind.phenotype
assert individual.ref_depth == 10
assert individual.alt_depth == 7
assert individual.depth == 17
assert individual.genotype_quality == 99
def test_check_gemini_db(gemini_path, vcf_file):
adapter = GeminiPlugin()
adapter.db = gemini_path
assert adapter.test_gemini_db()
adapter.db = vcf_file
with pytest.raises(DatabaseError):
adapter.test_gemini_db()
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'
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 browser_puzzle(args):
host = args.host
port = args.port
try:
# Puzzle browser plugin
from puzzle.server import factory as puzzle_app
from puzzle.plugins import GeminiPlugin
from puzzle.server.settings import BaseConfig
except ImportError as e:
raise ImportError("%s\nPlease 'pip install puzzle' if you want to run it\n" % e)
plugin = GeminiPlugin(db=args.db, vtype="sv")
root = os.path.expanduser("~/.puzzle")
BaseConfig.PUZZLE_BACKEND = plugin
BaseConfig.UPLOAD_DIR = os.path.join(root, 'resources')
puzzle_srv = puzzle_app.create_app(config_obj=BaseConfig)
webbrowser.open_new_tab("http://{}:{}".format(host, port))
run(puzzle_srv, host=host, port=port)
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_setup_with_variant_type(gemini_path):
adapter = GeminiPlugin('sv')
assert adapter.variant_type == 'sv'
def test_add_exac_no_frequency(self, variant):
adapter = GeminiPlugin()
gemini_variant = {'aaf_exac_all': None}
adapter._add_exac(variant, gemini_variant)
assert len(variant.frequencies) == 0
def test_add_exac_no_frequency(self, variant):
adapter = GeminiPlugin()
gemini_variant = {'aaf_exac_all':None}
adapter._add_exac(variant, gemini_variant)
assert len(variant.frequencies) == 0
