Filters API

Advanced Filtering System for VarAnnote v1.0.0

Provides comprehensive variant filtering capabilities including: - Quality score filtering - Population frequency thresholds - Clinical significance filters - Gene-based filtering - Consequence type filtering - Custom filter expressions

class varannote.utils.filters.FilterOperator(value)

Bases: Enum

Filter operators

EQUALS = '=='

NOT_EQUALS = '!='

GREATER_THAN = '>'

GREATER_EQUAL = '>='

LESS_THAN = '<'

LESS_EQUAL = '<='

CONTAINS = 'contains'

NOT_CONTAINS = 'not_contains'

IN = 'in'

NOT_IN = 'not_in'

REGEX = 'regex'

IS_NULL = 'is_null'

IS_NOT_NULL = 'is_not_null'

class varannote.utils.filters.ClinicalSignificance(value)

Bases: Enum

Clinical significance categories

PATHOGENIC = 'Pathogenic'

LIKELY_PATHOGENIC = 'Likely_pathogenic'

UNCERTAIN_SIGNIFICANCE = 'Uncertain_significance'

LIKELY_BENIGN = 'Likely_benign'

BENIGN = 'Benign'

CONFLICTING = 'Conflicting'

NOT_PROVIDED = 'Not_provided'

class varannote.utils.filters.FilterRule(field, operator, value, description=None)

Bases: object

Individual filter rule

field: str

operator: FilterOperator

value: Any

description: Optional[str] = None

__init__(field, operator, value, description=None)

class varannote.utils.filters.FilterSet(name, rules, logic='AND', description=None, enabled=True)

Bases: object

Collection of filter rules with logic

name: str

rules: List[FilterRule]

logic: str = 'AND'

description: Optional[str] = None

enabled: bool = True

__init__(name, rules, logic='AND', description=None, enabled=True)

class varannote.utils.filters.VariantFilter

Bases: object

Advanced variant filtering system

Features: - Multiple filter criteria - Logical combinations (AND/OR) - Custom filter expressions - Predefined filter sets - Performance optimization

__init__()

Initialize variant filter

apply_filter(variants, filter_set)

Apply filter set to variants

Parameters:

• variants (List[Dict[str, Any]]) – List of variant dictionaries

• filter_set (FilterSet) – Filter set to apply

Return type:

List[Dict[str, Any]]

Returns:

Filtered list of variants

apply_multiple_filters(variants, filter_sets, combine_logic='AND')

Apply multiple filter sets

Parameters:

• variants (List[Dict[str, Any]]) – List of variant dictionaries

• filter_sets (List[FilterSet]) – List of filter sets to apply

• combine_logic (str) – How to combine filter sets (AND/OR)

Return type:

List[Dict[str, Any]]

Returns:

Filtered list of variants

create_quality_filter(min_quality=0.0, max_population_freq=1.0, include_uncertain=True)

Create quality-based filter set

Return type:

FilterSet

create_clinical_filter(significance_levels=None, exclude_benign=False, require_review=False)

Create clinical significance filter set

Return type:

FilterSet

create_gene_filter(gene_list=None, gene_types=None, exclude_intergenic=True)

Create gene-based filter set

Return type:

FilterSet

create_consequence_filter(consequence_types=None, severity_threshold='moderate')

Create consequence-based filter set

Return type:

FilterSet

create_custom_filter(expression)

Create custom filter from expression

Parameters:

expression (str) – Filter expression (e.g., “quality_score > 0.8 AND population_frequency < 0.01”)

Return type:

FilterSet

Returns:

FilterSet object

get_predefined_filter(name)

Get predefined filter set by name

Return type:

Optional[FilterSet]

list_predefined_filters()

List available predefined filter names

Return type:

List[str]

get_filter_statistics(variants, filter_set)

Get statistics about filter application

Return type:

Dict[str, Any]

varannote.utils.filters.get_variant_filter()

Get global variant filter instance

Return type:

VariantFilter

varannote.utils.filters.apply_quality_filter(variants, min_quality=0.0, max_population_freq=1.0)

Apply quality filter to variants

Return type:

List[Dict[str, Any]]

varannote.utils.filters.apply_clinical_filter(variants, significance_levels=None)

Apply clinical significance filter to variants

Return type:

List[Dict[str, Any]]

varannote.utils.filters.apply_predefined_filter(variants, filter_name)

Apply predefined filter to variants

Return type:

List[Dict[str, Any]]