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_daughter = individual.Individual(ind='1', family='1',mother='3', father='2', sex=2, 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)
self.recessive_family.add_individual(healthy_father)
self.recessive_family.add_individual(sick_daughter)
self.recessive_family.add_individual(healthy_mother)
self.x_recessive_dn_variant = {'CHROM':'X', 'POS':'5', 'ALT':'A', 'REF':'C', 'ID':'rs2230749', '1':'0/1', '2':'0/0', '3':'0/0'}
self.x_recessive_missing = {'CHROM':'X', 'POS':'10', 'ALT':'C', 'REF':'T', 'ID':'.', '1':'1/1', '2':'0/0', '3':'./.'}
self.x_recessive_variant = {'CHROM':'X', 'POS':'13', 'ALT':'A', 'REF':'C', 'ID':'rs2230749', '1':'1/1', '2':'0/0', '3':'0/1'}
self.not_x_recessive = {'CHROM':'X', 'POS':'15', 'ALT':'C', 'REF':'T', 'ID':'.', '1':'0/1', '2':'./.', '3':'1/1'}
#This batch simulates one genewith all above variants:
batch = {'ABC':{'X_5_A_C':self.x_recessive_dn_variant, 'X_10_C_T':self.x_recessive_missing,
'X_13_A_C':self.x_recessive_variant, 'X_15_C_T':self.not_x_recessive}}
genetic_models.check_genetic_models(batch, self.recessive_family, verbose=True)
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)
self.recessive_family.add_individual(healthy_father)
self.recessive_family.add_individual(sick_son)
self.recessive_family.add_individual(healthy_mother)
interval = [1,100, '1']
intervals = {ind_id:interval_tree.IntervalTree([interval], 1, 100) for ind_id in self.recessive_family.individuals}
#Setup two variants with only autosomal recessive pattern
self.recessive_comp_simple_1 = {'CHROM':'1', 'POS':'5', 'ALT':'A', 'REF':'C', 'ID':'rs2230749',
'1':'0|1', '2':'0|1', '3':'0|0'}
self.recessive_comp_simple_2 = {'CHROM':'1', 'POS':'10', 'ALT':'C', 'REF':'T', 'ID':'.',
'1':'1|0', '2':'0|0', '3':'0|1'}
#Setup two variants that parents have but on same allele
self.recessive_comp_not_simple_1 = {'CHROM':'1', 'POS':'15', 'ALT':'A', 'REF':'C', 'ID':'.',
'1':'0|1', '2':'0|1', '3':'1|0'}
self.recessive_comp_not_simple_2 = {'CHROM':'1', 'POS':'17', 'ALT':'C', 'REF':'T', 'ID':'.',
'1':'1|0', '2':'0|1', '3':'1|0'}
#This one should not be recessive since the sick have both variants on same allele:
self.not_recessive_comp_1 = {'CHROM':'1', 'POS':'27', 'ALT':'G', 'REF':'T', 'ID':'.',
'1':'0|1', '2':'0|1', '3':'0|0'}
self.not_recessive_comp_2 = {'CHROM':'1', 'POS':'35', 'ALT':'C', 'REF':'T', 'ID':'.',
'1':'0|1', '2':'0|0', '3':'0|1'}
#Setup two variants that parents have but on same allele
self.recessive_comp_missing_1 = {'CHROM':'1', 'POS':'45', 'ALT':'A', 'REF':'C', 'ID':'.',
'1':'0|1', '2':'./.', '3':'1|0'}
self.recessive_comp_missing_2 = {'CHROM':'1', 'POS':'47', 'ALT':'C', 'REF':'T', 'ID':'.',
'1':'1|0', '2':'0|1', '3':'1|0'}
batch = {'ABC':{'1_5_A_C':self.recessive_comp_simple_1, '1_10_C_T':self.recessive_comp_simple_2},
'BBC':{'1_15_A_C':self.recessive_comp_not_simple_1, '1_17_C_T':self.recessive_comp_not_simple_2},
'CBC':{'1_27_G_T':self.not_recessive_comp_1, '1_35_C_T':self.not_recessive_comp_2},
'DBC':{'1_45_A_C':self.recessive_comp_missing_1, '1_47_C_T':self.recessive_comp_missing_2}
}
batch['haploblocks'] = intervals
genetic_models.check_genetic_models(batch, self.recessive_family, phased=True)
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.random_individual = individual.Individual(ind='0')
def setup_class(self):
"""Setup a simple family with family id 1, sick daughter id 1, healthy father id 2, healthy mother id 3"""
# Create a family
self.fam_id = '1'
self.family = family.Family(family_id=self.fam_id)
# Create a sick daughter:
self.daughter = individual.Individual(ind='1',
family=self.fam_id,
mother='3',
father='2',
sex=2,
phenotype=2)
# Create a healthy son:
self.son = individual.Individual(ind='4',
family=self.fam_id,
mother='3',
father='2',
sex=1,
phenotype=1)
# Create a healthy father
self.father = individual.Individual(ind='2',
family=self.fam_id,
mother='0',
father='0',
sex=1,
phenotype=1)
# Create a healthy mother
self.mother = individual.Individual(ind='3',
family=self.fam_id,
mother='0',
father='0',
sex=2,
phenotype=1)
self.family.add_individual(self.daughter)
self.family.add_individual(self.son)
self.family.add_individual(self.father)
self.family.add_individual(self.mother)
self.family.family_check()
def main():
from ped_parser import family, individual
from interval_tree import interval_tree
from vcf_parser import genotype
duo_family = family.Family(family_id = '1')
sick_son = individual.Individual(ind='1', family='1',mother='3', father='0', sex=1, phenotype=2)
healthy_mother = individual.Individual(ind='3', family='1',mother='0', father='0', sex=2, phenotype=1)
duo_family.add_individual(sick_son)
duo_family.add_individual(healthy_mother)
pp(duo_family.individuals)
intervals = {ind_id:interval_tree.IntervalTree([[1,100, '1']], 1, 100) for ind_id in duo_family.individuals}
pp(intervals)
#Setup two variants with autosomal recessive compound pattern
recessive_comp_simple_1 = {'CHROM':'1', 'POS':'5', 'ALT':'A', 'REF':'C', 'ID':'rs2230749',
'1':'0|1', '3':'0|0'}
genotypes = {'1':genotype.Genotype('0|1'), '3':genotype.Genotype('0|0')}
recessive_comp_simple_1['genotypes'] = genotypes
recessive_comp_simple_2 = {'CHROM':'1', 'POS':'10', 'ALT':'C', 'REF':'T', 'ID':'.',
'1':'1|0', '3':'0|1'}
genotypes = {'1':genotype.Genotype('1|0'), '3':genotype.Genotype('0|1')}
recessive_comp_simple_2['genotypes'] = genotypes
batch = {'ABC':{'1_5_A_C':recessive_comp_simple_1, '1_10_C_T':recessive_comp_simple_2}}
batch['haploblocks'] = intervals
check_genetic_models(batch, duo_family, phased=True)
for gene in batch:
# pp(batch[gene])
for variant in batch[gene]:
pp(batch[gene][variant])
for ind in batch[gene][variant]['genotypes']:
print(ind, batch[gene][variant]['genotypes'][ind].__dict__)
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)
self.recessive_family.add_individual(healthy_father)
self.recessive_family.add_individual(sick_son)
self.recessive_family.add_individual(healthy_mother)
#Setup two variants with only autosomal recessive pattern
self.recessive_comp_variant_1 = {'CHROM':'1', 'POS':'5', 'ALT':'A', 'REF':'C', 'ID':'rs2230749', '1':'0/1', '2':'0/1', '3':'0/0'}
self.recessive_comp_variant_2 = {'CHROM':'1', 'POS':'10', 'ALT':'C', 'REF':'T', 'ID':'.', '1':'0/1', '2':'0/0', '3':'0/1'}
#This one should not be recessive since both parents will have a combination:
self.not_recessive_comp = {'CHROM':'1', 'POS':'7', 'ALT':'G', 'REF':'T', 'ID':'.', '1':'0/1', '2':'0/1', '3':'0/1'}
self.recessive_comp_missing = {'CHROM':'1', 'POS':'15', 'ALT':'C', 'REF':'T', 'ID':'.', '1':'0/1', '2':'0/1', '3':'./.'}
batch = {'ABC':{'1_5_A_C':self.recessive_comp_variant_1, '1_10_C_T':self.recessive_comp_variant_2, '1_7_G_T':self.not_recessive_comp},
'BBC':{'1_10_C_T':self.recessive_comp_variant_2, '1_15_C_T':self.recessive_comp_missing}}
genetic_models.check_genetic_models(batch, 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.dominant_family = family.Family(family_id='1')
sick_son = individual.Individual(ind='1',
family='1',
mother='3',
father='2',
sex=1,
phenotype=2)
sick_father = individual.Individual(ind='2',
family='1',
mother='0',
father='0',
sex=1,
phenotype=2)
healthy_mother = individual.Individual(ind='3',
family='1',
mother='0',
father='0',
sex=2,
phenotype=1)
self.dominant_family.add_individual(sick_father)
self.dominant_family.add_individual(sick_son)
self.dominant_family.add_individual(healthy_mother)
self.dominant_variant = {
'CHROM': '1',
'POS': '5',
'ALT': 'A',
'REF': 'C',
'ID': 'rs2230749',
'1': '0/1',
'2': '0/1',
'3': '0/0'
}
self.dominant_missing = {
'CHROM': '1',
'POS': '10',
'ALT': 'C',
'REF': 'T',
'ID': '.',
'1': '0/1',
'2': './.',
'3': '0/0'
}
self.not_dominant = {
'CHROM': '1',
'POS': '15',
'ALT': 'C',
'REF': 'T',
'ID': '.',
'1': '0/1',
'2': '0/1',
'3': '0/1'
}
#This batch simulates two genes, one variant is present in both genes
batch = {
'ABC': {
'1_5_A_C': self.dominant_variant,
'1_10_C_T': self.dominant_missing,
'1_15_C_T': self.not_dominant
}
}
genetic_models.check_genetic_models(batch,
self.dominant_family,
verbose=True)
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)
self.recessive_family.add_individual(healthy_father)
self.recessive_family.add_individual(sick_son)
self.recessive_family.add_individual(healthy_mother)
#Setup two variants with only autosomal recessive pattern
self.recessive_variant = {
'CHROM': '1',
'POS': '5',
'ALT': 'A',
'REF': 'C',
'ID': 'rs2230749',
'1': '1/1',
'2': '0/1',
'3': '0/1'
}
self.recessive_dn = {
'CHROM': '1',
'POS': '7',
'ALT': 'G',
'REF': 'T',
'ID': '.',
'1': '1/1',
'2': '0/1',
'3': '0/0'
}
self.recessive_missing = {
'CHROM': '1',
'POS': '10',
'ALT': 'C',
'REF': 'T',
'ID': '.',
'1': '1/1',
'2': './.',
'3': '0/1'
}
self.not_recessive = {
'CHROM': '1',
'POS': '15',
'ALT': 'C',
'REF': 'T',
'ID': '.',
'1': '0/1',
'2': '0/1',
'3': './.'
}
#This batch simulates two genes, one variant is present in both genes
batch = {
'ABC': {
'1_5_A_C': self.recessive_variant,
'1_10_C_T': self.recessive_missing,
'1_7_G_T': self.recessive_dn
},
'BBC': {
'1_10_C_T': self.recessive_missing,
'1_15_C_T': self.not_recessive
}
}
genetic_models.check_genetic_models(batch, self.recessive_family)