Module ImportFrom alias ImportFrom alias ImportFrom alias Assign NameStore Str FunctionDef arguments args NameParam NameParam defaults NameLoad NameLoad body Expr Str Assign NameStore NameLoad If NameLoad body Assign NameStore Call NameLoad Call NameLoad NameLoad Str orelse If NameLoad body Assign NameStore Call NameLoad NameLoad Return NameLoad decorator_list FunctionDef arguments args defaults body Expr Str Assign NameStore ListLoad Str Str Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Dict Str Dict Assign SubscriptStore SubscriptLoad NameLoad Index Str Index Str Call NameLoad Dict Str Str Assert CompareEq Call NameLoad keyword NameLoad keyword NameLoad NameLoad decorator_list FunctionDef arguments args defaults body Expr Str Assign NameStore ListLoad Str Str Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Dict Str Dict Assign SubscriptStore SubscriptLoad NameLoad Index Str Index Str Call NameLoad Dict Str Str Assert CompareEq Call NameLoad keyword NameLoad keyword NameLoad NameLoad decorator_list FunctionDef arguments args defaults body Expr Str Assign NameStore ListLoad Str Str Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Dict Str Dict Assign SubscriptStore SubscriptLoad NameLoad Index Str Index Str Call NameLoad Dict Str Str Assert CompareEq Call NameLoad keyword NameLoad keyword NameLoad NameLoad decorator_list FunctionDef arguments args defaults body Expr Str Assign NameStore ListLoad Str Str Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Dict Str Dict Assign SubscriptStore SubscriptLoad NameLoad Index Str Index Str Call NameLoad Dict Str Str Assert CompareEq Call NameLoad keyword NameLoad keyword NameLoad NameLoad decorator_list FunctionDef arguments args defaults body Expr Str Assign NameStore ListLoad Str Str Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Dict Str Dict Assign SubscriptStore SubscriptLoad NameLoad Index Str Index Str Call NameLoad Dict Str Str Assert CompareEq Call NameLoad keyword NameLoad keyword NameLoad NameLoad decorator_list FunctionDef arguments args defaults body Expr Str Assign NameStore ListLoad Str Str Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Dict Str Dict Assign SubscriptStore SubscriptLoad NameLoad Index Str Index Str Call NameLoad Dict Str Str Assert CompareEq Call NameLoad keyword NameLoad keyword NameLoad NameLoad decorator_list FunctionDef arguments args defaults body Expr Str Assign NameStore ListLoad Str Str Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Dict Str Dict Assign SubscriptStore SubscriptLoad NameLoad Index Str Index Str Call NameLoad Dict Str Str Assert CompareEq Call NameLoad keyword NameLoad keyword NameLoad NameLoad decorator_list FunctionDef arguments args defaults body Expr Str Assign NameStore ListLoad Str Str Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Dict Str Dict Assign SubscriptStore SubscriptLoad NameLoad Index Str Index Str Call NameLoad Dict Str Str Assert CompareEq Call NameLoad keyword NameLoad keyword NameLoad keyword NameLoad NameLoad decorator_list FunctionDef arguments args defaults body Expr Str Assign NameStore ListLoad Str Str Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Dict Str Dict Assign SubscriptStore SubscriptLoad NameLoad Index Str Index Str Call NameLoad Dict Str Str Assert CompareEq Call NameLoad keyword NameLoad keyword NameLoad NameLoad decorator_list FunctionDef arguments args defaults body Expr Str Assign NameStore ListLoad Str Str Assign NameStore Call NameLoad keyword NameLoad Assign NameStore Dict Str Dict Assign SubscriptStore SubscriptLoad NameLoad Index Str Index Str Call NameLoad Dict Str Str Assert CompareEq Call NameLoad keyword NameLoad keyword NameLoad NameLoad decorator_list
N/A genmod.annotate_models.models check_X_recessive genmod.vcf_tools Genotype ped_parser FamilyParser N/A FAMILY_FILE tests/fixtures/recessive_trio.ped get_family N/A N/A family_file family_lines N/A None None N/A N/A Return a family object
    
     N/A family None N/A family_file N/A N/A family N/A FamilyParser N/A open family_file r N/A N/A family_lines N/A N/A family N/A FamilyParser family_lines N/A family N/A test_x_affected_recessive_male N/A N/A N/A N/A N/A Test a sick male
     N/A family_lines N/A #FamilyID	SampleID	Father	Mother	Sex	Phenotype
 1	proband	0	0	1	2
 N/A family N/A get_family family_lines family_lines N/A recessive_variant N/A genotypes N/A N/A N/A N/A recessive_variant N/A genotypes N/A proband N/A Genotype N/A GT 0/1 N/A N/A N/A check_X_recessive variant recessive_variant family family True N/A test_x_affected_recessive_female N/A N/A N/A N/A N/A Test a sick heterozygote female
    
    Females needs to bo hom alt to follow pattern
     N/A family_lines N/A #FamilyID	SampleID	Father	Mother	Sex	Phenotype
 1	proband	0	0	2	2
 N/A family N/A get_family family_lines family_lines N/A recessive_variant N/A genotypes N/A N/A N/A N/A recessive_variant N/A genotypes N/A proband N/A Genotype N/A GT 0/1 N/A N/A N/A check_X_recessive variant recessive_variant family family False N/A test_x_affected_homozygote_male N/A N/A N/A N/A N/A Test an affected homozygote male N/A family_lines N/A #FamilyID	SampleID	Father	Mother	Sex	Phenotype
 1	proband	0	0	1	2
 N/A family N/A get_family family_lines family_lines N/A homozygote_variant N/A genotypes N/A N/A N/A N/A homozygote_variant N/A genotypes N/A proband N/A Genotype N/A GT 1/1 N/A N/A N/A check_X_recessive variant homozygote_variant family family True N/A test_x_affected_homozygote_female N/A N/A N/A N/A N/A Test an affected homozygote male N/A family_lines N/A #FamilyID	SampleID	Father	Mother	Sex	Phenotype
 1	proband	0	0	2	2
 N/A family N/A get_family family_lines family_lines N/A homozygote_variant N/A genotypes N/A N/A N/A N/A homozygote_variant N/A genotypes N/A proband N/A Genotype N/A GT 1/1 N/A N/A N/A check_X_recessive variant homozygote_variant family family True N/A test_x_affected_male_ref_call N/A N/A N/A N/A N/A Test an affected ref call male N/A family_lines N/A #FamilyID	SampleID	Father	Mother	Sex	Phenotype
 1	proband	0	0	1	2
 N/A family N/A get_family family_lines family_lines N/A homozygote_variant N/A genotypes N/A N/A N/A N/A homozygote_variant N/A genotypes N/A proband N/A Genotype N/A GT 0/0 N/A N/A N/A check_X_recessive variant homozygote_variant family family False N/A test_x_affected_female_ref_call N/A N/A N/A N/A N/A Test an affected ref call male N/A family_lines N/A #FamilyID	SampleID	Father	Mother	Sex	Phenotype
 1	proband	0	0	2	2
 N/A family N/A get_family family_lines family_lines N/A homozygote_variant N/A genotypes N/A N/A N/A N/A homozygote_variant N/A genotypes N/A proband N/A Genotype N/A GT 0/0 N/A N/A N/A check_X_recessive variant homozygote_variant family family False N/A test_x_affected_no_call_male N/A N/A N/A N/A N/A Test a sick male with no gt call
    
    This should be true since there is no information that contradicts the model
     N/A family_lines N/A #FamilyID	SampleID	Father	Mother	Sex	Phenotype
 1	proband	0	0	1	2
 N/A family N/A get_family family_lines family_lines N/A no_call_variant N/A genotypes N/A N/A N/A N/A no_call_variant N/A genotypes N/A proband N/A Genotype N/A GT ./. N/A N/A N/A check_X_recessive variant no_call_variant family family True N/A test_x_affected_no_call_male_strict N/A N/A N/A N/A N/A Test a sick male with no gt call
    
    This should not be true since we allways need 'proof'
    for an inheritance pattern if strict mode.
     N/A family_lines N/A #FamilyID	SampleID	Father	Mother	Sex	Phenotype
 1	proband	0	0	1	2
 N/A family N/A get_family family_lines family_lines N/A no_call_variant N/A genotypes N/A N/A N/A N/A no_call_variant N/A genotypes N/A proband N/A Genotype N/A GT ./. N/A N/A N/A check_X_recessive variant no_call_variant family family strict True False N/A test_x_healthy_recessive_male N/A N/A N/A N/A N/A Test a healthy recessive male
     N/A family_lines N/A #FamilyID	SampleID	Father	Mother	Sex	Phenotype
 1	proband	0	0	1	1
 N/A family N/A get_family family_lines family_lines N/A recessive_variant N/A genotypes N/A N/A N/A N/A recessive_variant N/A genotypes N/A proband N/A Genotype N/A GT 0/1 N/A N/A N/A check_X_recessive variant recessive_variant family family False N/A test_x_healthy_recessive_female N/A N/A N/A N/A N/A Test a healthy heterozygote female
    
    Females needs to bo hom alt to follow pattern
     N/A family_lines N/A #FamilyID	SampleID	Father	Mother	Sex	Phenotype
 1	proband	0	0	2	1
 N/A family N/A get_family family_lines family_lines N/A recessive_variant N/A genotypes N/A N/A N/A N/A recessive_variant N/A genotypes N/A proband N/A Genotype N/A GT 0/1 N/A N/A N/A check_X_recessive variant recessive_variant family family True N/A