def setup_class(self):
"""Setup a simple family with family id 1, sick daughter id 1, healthy father id 2, healthy mother id 3"""
self.daughter = individual.Individual(ind='1', family='1', mother='3', father='2', sex=2, phenotype=2)
self.father = individual.Individual(ind='2', family='1', mother='0', father='0', sex=1, phenotype=1)
self.mother = individual.Individual(ind='3', family='1', mother='0', father='0', sex=2, phenotype=1)
self.daughter_genotypes = {}
self.father_genotypes = {}
self.mother_genotypes = {}
self.daughter_genotypes['1_1_T_A'] = genotype.Genotype(GT='0/1')
self.daughter_genotypes['1_3_A_C'] = genotype.Genotype(GT='1/1')
self.father_genotypes['1_1_T_A'] = genotype.Genotype(GT='0/0')
self.father_genotypes['1_3_A_C'] = genotype.Genotype(GT='0/1')
self.mother_genotypes['1_1_T_A'] = genotype.Genotype(GT='./.')
self.mother_genotypes['1_3_A_C'] = genotype.Genotype(GT='0/1')
def setup_class(self):
"""Setup a simple family with family id 1, sick daughter id 1, healthy father id 2, healthy mother id 3"""
self.family = family.Family(family_id='1') # Create a family
self.daughter = individual.Individual(
ind='1', family='1', mother='3', father='2', sex=2,
phenotype=2) # Create a sick daughter
self.father = individual.Individual(
ind='2', family='1', mother='0', father='0', sex=1,
phenotype=1) # Create a healthy father
self.mother = individual.Individual(
ind='3', family='1', mother='0', father='0', sex=2,
phenotype=1) # Create a healthy mother
self.family.add_individual(self.daughter)
self.family.add_individual(self.father)
self.family.add_individual(self.mother)
def setup_class(self):
"""Setup a simple family with family id 1, sick son id 1,
healthy father id 2, healthy mother id 3"""
# Setup family with sick kid, sick father and healthy mother:
self.recessive_family = family.Family(family_id = '1')
sick_son = individual.Individual(ind='1', family='1',mother='3', father='2', sex=1, phenotype=2)
healthy_father = individual.Individual(ind='2', family='1',mother='0', father='0', sex=1, phenotype=1)
healthy_mother = individual.Individual(ind='3', family='1',mother='0', father='0', sex=2, phenotype=1)
#Setup variant with only autosomal dominant de novo pattern
self.recessive_dn_variant = genetic_variant.Variant(chrom = '1', start = 5, stop=5, alternative = 'A',
reference = 'C', identity = 'rs2230749')
sick_son.add_genotype(self.recessive_dn_variant.variant_id, genotype.Genotype(GT='1/1'))
healthy_father.add_genotype(self.recessive_dn_variant.variant_id, genotype.Genotype(GT='0/1'))
healthy_mother.add_genotype(self.recessive_dn_variant.variant_id, genotype.Genotype(GT='0/0'))
#Setup variant with only autosomal recessive pattern
self.recessive_variant = genetic_variant.Variant(chrom = '1', start = 10, stop=10, alternative = 'C',
reference = 'T')
sick_son.add_genotype(self.recessive_variant.variant_id, genotype.Genotype(GT='1/1'))
healthy_father.add_genotype(self.recessive_variant.variant_id, genotype.Genotype(GT='0/1'))
healthy_mother.add_genotype(self.recessive_variant.variant_id, genotype.Genotype(GT='0/1'))
#Setup potential recessive but does not follow any patterns
self.almost_recessive_variant = genetic_variant.Variant(chrom = '1', start = 20, stop=20, alternative = 'C',
reference = 'T')
sick_son.add_genotype(self.almost_recessive_variant.variant_id, genotype.Genotype(GT='./.'))
healthy_father.add_genotype(self.almost_recessive_variant.variant_id, genotype.Genotype(GT='0/1'))
healthy_mother.add_genotype(self.almost_recessive_variant.variant_id, genotype.Genotype(GT='0/1'))
self.recessive_family.add_individual(healthy_father)
self.recessive_family.add_individual(sick_son)
self.recessive_family.add_individual(healthy_mother)
self.recessive_family.add_variant(self.recessive_dn_variant)
self.recessive_family.add_variant(self.recessive_variant)
self.recessive_family.add_variant(self.almost_recessive_variant)
self.my_healthy_father_model = genetic_models.genetic_models(self.recessive_family)
def setup_class(self):
"""Setup a simple family with family id 1, sick son id 1,
healthy father id 2, healthy mother id 3"""
# Setup family with sick kid, sick father and healthy mother:
self.recessive_family = family.Family(family_id = '1')
sick_son = individual.Individual(ind='1', family='1',mother='3', father='2', sex=1, phenotype=2)
healthy_father = individual.Individual(ind='2', family='1',mother='0', father='0', sex=1, phenotype=1)
healthy_mother = individual.Individual(ind='3', family='1',mother='0', father='0', sex=2, phenotype=1)
#Setup two variants with only autosomal recessive pattern
self.recessive_comp_variant_1 = genetic_variant.Variant(chrom = '1', start = 5, stop=5, alternative = 'A',
reference = 'C', identity = 'rs2230749',
all_info={'Ensemble_GeneID':'ENSG00000187634;'})
self.recessive_comp_variant_2 = genetic_variant.Variant(chrom = '1', start = 10, stop=10, alternative = 'C',
reference = 'T', identity = '.',
all_info={'Ensemble_GeneID':'ENSG00000187634;'})
sick_son.add_genotype(self.recessive_comp_variant_1.variant_id, genotype.Genotype(GT='0/1'))
healthy_father.add_genotype(self.recessive_comp_variant_1.variant_id, genotype.Genotype(GT='0/1'))
healthy_mother.add_genotype(self.recessive_comp_variant_1.variant_id, genotype.Genotype(GT='0/0'))
sick_son.add_genotype(self.recessive_comp_variant_2.variant_id, genotype.Genotype(GT='0/1'))
healthy_father.add_genotype(self.recessive_comp_variant_2.variant_id, genotype.Genotype(GT='0/0'))
healthy_mother.add_genotype(self.recessive_comp_variant_2.variant_id, genotype.Genotype(GT='0/1'))
self.recessive_family.add_individual(healthy_father)
self.recessive_family.add_individual(sick_son)
self.recessive_family.add_individual(healthy_mother)
self.recessive_family.add_variant(self.recessive_comp_variant_1)
self.recessive_family.add_variant(self.recessive_comp_variant_2)
self.my_healthy_father_model = genetic_models.genetic_models(self.recessive_family)
for variant in self.recessive_family.variants:
self.recessive_family.variants[variant].check_models()
def setup_class(self):
"""Setup a simple family with family id 1, sick daughter id 1,
healthy father id 2, healthy mother id 3"""
# Setup family with sick kid, sick father and healthy mother:
self.sick_father_family = family.Family(family_id='2')
sick_daugther = individual.Individual(ind='1',
family='2',
mother='3',
father='2',
sex=2,
phenotype=2)
sick_father = individual.Individual(ind='2',
family='2',
mother='0',
father='0',
sex=1,
phenotype=2)
healthy_mother = individual.Individual(ind='3',
family='2',
mother='0',
father='0',
sex=2,
phenotype=1)
#Setup variant with only autosomal dominant pattern
self.dominant_variant = genetic_variant.Variant(chrom='1',
start=5,
stop=5,
alternative='A',
reference='C',
identity='rs2230749')
sick_daugther.add_genotype(self.dominant_variant.variant_id,
genotype.Genotype(GT='0/1'))
sick_father.add_genotype(self.dominant_variant.variant_id,
genotype.Genotype(GT='0/1'))
healthy_mother.add_genotype(self.dominant_variant.variant_id,
genotype.Genotype(GT='0/0'))
#Setup variant with only autosomal recessive pattern(Should not work here)
self.recessive_variant = genetic_variant.Variant(chrom='1',
start=10,
stop=10,
alternative='C',
reference='T')
sick_daugther.add_genotype(self.recessive_variant.variant_id,
genotype.Genotype(GT='1/1'))
sick_father.add_genotype(self.recessive_variant.variant_id,
genotype.Genotype(GT='0/1'))
healthy_mother.add_genotype(self.recessive_variant.variant_id,
genotype.Genotype(GT='0/1'))
self.sick_father_family.add_individual(sick_father)
self.sick_father_family.add_individual(sick_daugther)
self.sick_father_family.add_individual(healthy_mother)
self.sick_father_family.add_variant(self.dominant_variant)
self.sick_father_family.add_variant(self.recessive_variant)
self.my_sick_father_model = genetic_models.genetic_models(
self.sick_father_family)
def setup_class(self):
"""Setup a simple family with family id 1, sick son id 1,
healthy father id 2, healthy mother id 3"""
# Setup family with sick kid, sick father and healthy mother:
self.recessive_family = family.Family(family_id='1')
sick_son = individual.Individual(ind='1',
family='1',
mother='3',
father='2',
sex=1,
phenotype=2)
healthy_father = individual.Individual(ind='2',
family='1',
mother='0',
father='0',
sex=1,
phenotype=1)
healthy_mother = individual.Individual(ind='3',
family='1',
mother='0',
father='0',
sex=2,
phenotype=1)
#Setup a variant where all are homozygote alternative
self.homozygote_alternative = genetic_variant.Variant(
chrom='1',
start=5,
stop=5,
alternative='A',
reference='C',
identity='rs2230749',
all_info={'Ensemble_GeneID': 'ENSG00000187634;'})
sick_son.add_genotype(self.homozygote_alternative.variant_id,
genotype.Genotype(GT='1/1'))
healthy_father.add_genotype(self.homozygote_alternative.variant_id,
genotype.Genotype(GT='1/1'))
healthy_mother.add_genotype(self.homozygote_alternative.variant_id,
genotype.Genotype(GT='1/0'))
#Setup a variant that is recessive de novo
self.recessive_dn = genetic_variant.Variant(
chrom='1',
start=6,
stop=6,
alternative='C',
reference='T',
identity='.',
all_info={'Ensemble_GeneID': 'ENSG00000187634;'})
sick_son.add_genotype(self.recessive_dn.variant_id,
genotype.Genotype(GT='1/1'))
healthy_father.add_genotype(self.recessive_dn.variant_id,
genotype.Genotype(GT='./.'))
healthy_mother.add_genotype(self.recessive_dn.variant_id,
genotype.Genotype(GT='0/1'))
self.recessive_family.add_individual(healthy_father)
self.recessive_family.add_individual(sick_son)
self.recessive_family.add_individual(healthy_mother)
self.recessive_family.add_variant(self.homozygote_alternative)
self.recessive_family.add_variant(self.recessive_dn)
self.my_healthy_father_model = genetic_models.genetic_models(
self.recessive_family)
for variant in self.recessive_family.variants:
self.recessive_family.variants[variant].check_models()