def run(self):
"""Run the consuming"""
proc_name = self.name
if self.verbosity:
print('%s: Starting!' % proc_name)
while True:
# A batch is a dictionary on the form {gene:{variant_id:variant_dict}}
next_batch = self.task_queue.get()
# if self.verbosity:
# if self.results_queue.full():
# print('Batch results queue Full! %s' % proc_name)
# if self.task_queue.full():
# print('Variant queue full! %s' % proc_name)
if next_batch is None:
self.task_queue.task_done()
if self.verbosity:
print('%s: Exiting' % proc_name)
break
genetic_models.check_genetic_models(next_batch, self.family,
self.verbosity, self.phased,
proc_name)
# Make shure we only have one copy of each variant:
fixed_variants = self.fix_variants(next_batch)
# Now we want to make versions of the variants that are ready for printing.
self.make_print_version(fixed_variants)
self.results_queue.put(fixed_variants)
self.task_queue.task_done()
return
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)
#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)
def run(self):
"""Run the consuming"""
proc_name = self.name
if self.verbosity:
print('%s: Starting!' % proc_name)
while True:
# A batch is a dictionary on the form {gene:{variant_id:variant_dict}}
next_batch = self.task_queue.get()
# if self.verbosity:
# if self.results_queue.full():
# print('Batch results queue Full! %s' % proc_name)
# if self.task_queue.full():
# print('Variant queue full! %s' % proc_name)
if next_batch is None:
self.task_queue.task_done()
if self.verbosity:
print('%s: Exiting' % proc_name)
break
genetic_models.check_genetic_models(next_batch, self.family, self.verbosity, self.phased, proc_name)
# Make shure we only have one copy of each variant:
fixed_variants = self.fix_variants(next_batch)
# Now we want to make versions of the variants that are ready for printing.
self.make_print_version(fixed_variants)
self.results_queue.put(fixed_variants)
self.task_queue.task_done()
return
def setup_class(self):
"""Setup a simple family with family id 1, sick son id 1 and a healthy mother with id 3"""
# Setup family with sick kid, sick father and healthy mother:
self.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)
self.duo_family.add_individual(sick_son)
self.duo_family.add_individual(healthy_mother)
# This is a dummy phased interval:
interval = [1,100, '1']
intervals = {ind_id:interval_tree.IntervalTree([interval], 1, 100) for ind_id in self.duo_family.individuals}
#Setup two variants with autosomal recessive compound pattern
self.recessive_comp_simple_1 = {'CHROM':'1', 'POS':'5', 'ALT':'A', 'REF':'C', 'ID':'rs2230749',
'1':'0|1', '3':'0|0'}
self.recessive_comp_simple_2 = {'CHROM':'1', 'POS':'10', 'ALT':'C', 'REF':'T', 'ID':'.',
'1':'1|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', '3':'1|0'}
self.recessive_comp_not_simple_2 = {'CHROM':'1', 'POS':'17', 'ALT':'C', 'REF':'T', 'ID':'.',
'1':'1|0', '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', '3':'0|0'}
self.not_recessive_comp_2 = {'CHROM':'1', 'POS':'35', 'ALT':'C', 'REF':'T', 'ID':'.',
'1':'0|1', '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', '3':'0|0'}
self.recessive_comp_missing_2 = {'CHROM':'1', 'POS':'57', 'ALT':'C', 'REF':'T', 'ID':'.',
'1':'1|0', '3':'./.'}
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},
'DBC':{'1_45_A_C':self.recessive_comp_missing_1, '1_57_C_T':self.recessive_comp_missing_2},
'CBC':{'1_27_G_T':self.not_recessive_comp_1, '1_35_C_T':self.not_recessive_comp_2}
}
batch['haploblocks'] = intervals
pp(self.duo_family)
pp(batch)
pp(sys.path)
genetic_models.check_genetic_models(batch, self.duo_family, phased=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 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)