def setUp(self):
self.user = User.objects.create_user('*****@*****.**', 'test-user-password')
self.user.is_active = True
self.user.save()
population = ['EAS']
# Prepare GwasCatalogSnp
gwascatalog = [('00000001', 'Type 2 diabetes', 671, 'A', 1.5, population),
('00000001', 'Type 2 diabetes', 672, 'A', 1.5, population),
('00000001', 'Type 2 diabetes', 673, 'A', 1.5, population)]
for record in gwascatalog:
phenotype, _ = GwasCatalogPhenotype.objects.get_or_create(name=record[1])
GwasCatalogSnp(date_downloaded=today_with_tz,
pubmed_id=record[0],
phenotype=phenotype,
snp_id_current=record[2],
risk_allele_forward=record[3],
odds_ratio=record[4],
population=record[5]).save()
assert len(GwasCatalogPhenotype.objects.all()) == 1
assert len(GwasCatalogSnp.objects.all()) == 3
# Prepare Snp
freq = [(671, ['A','G'], [0.2,0.8], population),
(672, ['A','G'], [0.2,0.8], population),
(673, ['A','G'], [0.2,0.8], population)]
for record in freq:
Snp(snp_id_current=record[0],
allele=record[1],
freq=[Decimal(x) for x in record[2]],
population=record[3]).save()
assert len(Snp.objects.all()) == 3
# Prepare Genome
self.genome = Genome(owner=self.user, file_name='a.vcf', display_name='a.vcf', status=100, population=population[0])
self.genome.save()
assert self.genome.population == 'EAS'
def setUp(self):
self.user = User.objects.create_user("*****@*****.**", "test-user-password")
self.user.is_active = True
self.user.save()
population = ["EAS"]
# Prepare GwasCatalogSnp
gwascatalog = [
("00000001", "Type 2 diabetes", 671, "A", 1.5, population),
("00000001", "Type 2 diabetes", 672, "A", 1.5, population),
("00000001", "Type 2 diabetes", 673, "A", 1.5, population),
]
for record in gwascatalog:
phenotype, _ = GwasCatalogPhenotype.objects.get_or_create(name=record[1])
GwasCatalogSnp(
date_downloaded=today_with_tz,
pubmed_id=record[0],
phenotype=phenotype,
snp_id_current=record[2],
risk_allele_forward=record[3],
odds_ratio=record[4],
population=record[5],
).save()
assert len(GwasCatalogPhenotype.objects.all()) == 1
assert len(GwasCatalogSnp.objects.all()) == 3
# Prepare Snp
freq = [
(671, ["A", "G"], [0.2, 0.8], population),
(672, ["A", "G"], [0.2, 0.8], population),
(673, ["A", "G"], [0.2, 0.8], population),
]
for record in freq:
Snp(
snp_id_current=record[0], allele=record[1], freq=[Decimal(x) for x in record[2]], population=record[3]
).save()
assert len(Snp.objects.all()) == 3
# Prepare Genome
self.genome = Genome(
owner=self.user, file_name="a.vcf", display_name="a.vcf", status=100, population=population[0]
)
self.genome.save()
assert self.genome.population == "EAS"
class RiskReportModelTestCase(TestCase):
def setUp(self):
self.user = User.objects.create_user("*****@*****.**", "test-user-password")
self.user.is_active = True
self.user.save()
population = ["EAS"]
# Prepare GwasCatalogSnp
gwascatalog = [
("00000001", "Type 2 diabetes", 671, "A", 1.5, population),
("00000001", "Type 2 diabetes", 672, "A", 1.5, population),
("00000001", "Type 2 diabetes", 673, "A", 1.5, population),
]
for record in gwascatalog:
phenotype, _ = GwasCatalogPhenotype.objects.get_or_create(name=record[1])
GwasCatalogSnp(
date_downloaded=today_with_tz,
pubmed_id=record[0],
phenotype=phenotype,
snp_id_current=record[2],
risk_allele_forward=record[3],
odds_ratio=record[4],
population=record[5],
).save()
assert len(GwasCatalogPhenotype.objects.all()) == 1
assert len(GwasCatalogSnp.objects.all()) == 3
# Prepare Snp
freq = [
(671, ["A", "G"], [0.2, 0.8], population),
(672, ["A", "G"], [0.2, 0.8], population),
(673, ["A", "G"], [0.2, 0.8], population),
]
for record in freq:
Snp(
snp_id_current=record[0], allele=record[1], freq=[Decimal(x) for x in record[2]], population=record[3]
).save()
assert len(Snp.objects.all()) == 3
# Prepare Genome
self.genome = Genome(
owner=self.user, file_name="a.vcf", display_name="a.vcf", status=100, population=population[0]
)
self.genome.save()
assert self.genome.population == "EAS"
def test_create_riskreport_ok(self):
# TODO: add more phenotypes
phenotypes = ["Type 2 diabetes"]
# Prepare Genotype
gwas_snps = [(671, "{A,A}"), (672, "{A,G}"), (673, "{G,G}")]
for record in gwas_snps:
Genotype(genome=self.genome, rs_id_current=record[0], genotype=record[1]).save()
riskreport, _ = RiskReport.objects.get_or_create(genome=self.genome)
riskreport.create_riskreport()
phenotype_risk_repot = PhenotypeRiskReport.objects.filter(risk_report__genome=self.genome)
assert len(phenotype_risk_repot) == 1
assert phenotype_risk_repot.get(phenotype__name=phenotypes[0]).estimated_risk == Decimal("1.906")
snp_risk_reports = SnpRiskReport.objects.filter(phenotype_risk_report__risk_report__genome=self.genome)
assert len(snp_risk_reports) == 3
assert snp_risk_reports.get(evidence_snp__snp_id_current=671).estimated_risk == Decimal("1.860")
assert snp_risk_reports.get(evidence_snp__snp_id_current=672).estimated_risk == Decimal("1.240")
assert snp_risk_reports.get(evidence_snp__snp_id_current=673).estimated_risk == Decimal("0.8264")
class RiskReportModelTestCase(TestCase):
def setUp(self):
self.user = User.objects.create_user('*****@*****.**', 'test-user-password')
self.user.is_active = True
self.user.save()
population = ['EAS']
# Prepare GwasCatalogSnp
gwascatalog = [('00000001', 'Type 2 diabetes', 671, 'A', 1.5, population),
('00000001', 'Type 2 diabetes', 672, 'A', 1.5, population),
('00000001', 'Type 2 diabetes', 673, 'A', 1.5, population)]
for record in gwascatalog:
phenotype, _ = GwasCatalogPhenotype.objects.get_or_create(name=record[1])
GwasCatalogSnp(date_downloaded=today_with_tz,
pubmed_id=record[0],
phenotype=phenotype,
snp_id_current=record[2],
risk_allele_forward=record[3],
odds_ratio=record[4],
population=record[5]).save()
assert len(GwasCatalogPhenotype.objects.all()) == 1
assert len(GwasCatalogSnp.objects.all()) == 3
# Prepare Snp
freq = [(671, ['A','G'], [0.2,0.8], population),
(672, ['A','G'], [0.2,0.8], population),
(673, ['A','G'], [0.2,0.8], population)]
for record in freq:
Snp(snp_id_current=record[0],
allele=record[1],
freq=[Decimal(x) for x in record[2]],
population=record[3]).save()
assert len(Snp.objects.all()) == 3
# Prepare Genome
self.genome = Genome(owner=self.user, file_name='a.vcf', display_name='a.vcf', status=100, population=population[0])
self.genome.save()
assert self.genome.population == 'EAS'
def test_create_riskreport_ok(self):
# TODO: add more phenotypes
phenotypes = ['Type 2 diabetes']
# Prepare Genotype
gwas_snps = [(671, '{A,A}'),
(672, '{A,G}'),
(673, '{G,G}')]
for record in gwas_snps:
Genotype(genome=self.genome, rs_id_current=record[0], genotype=record[1]).save()
riskreport, _ = RiskReport.objects.get_or_create(genome=self.genome)
riskreport.create_riskreport()
phenotype_risk_repot = PhenotypeRiskReport.objects.filter(risk_report__genome=self.genome)
assert len(phenotype_risk_repot) == 1
assert phenotype_risk_repot.get(phenotype__name=phenotypes[0]).estimated_risk == Decimal('1.906')
snp_risk_reports = SnpRiskReport.objects.filter(phenotype_risk_report__risk_report__genome=self.genome)
assert len(snp_risk_reports) == 3
assert snp_risk_reports.get(evidence_snp__snp_id_current=671).estimated_risk == Decimal('1.860')
assert snp_risk_reports.get(evidence_snp__snp_id_current=672).estimated_risk == Decimal('1.240')
assert snp_risk_reports.get(evidence_snp__snp_id_current=673).estimated_risk == Decimal('0.8264')