Convert¶
Module for converting HGVS descriptions and lark parse trees to their equivalent dictionary models.
- class mutalyzer_hgvs_parser.convert.Converter(visit_tokens: bool = True)¶
Bases:
Transformer- AA(name: Token) dict¶
- COORDINATE_SYSTEM(name: Token) dict¶
- ID(name: Token) dict¶
- INVERTED(name: Token) dict¶
- OFFSET(name: Token) dict¶
- OUTSIDE_CDS(name: Token) dict¶
- P_SEQUENCE(name: Token) dict¶
- SEQUENCE(name: Token) dict¶
- UNKNOWN(name: Token) dict¶
- conversion(children: list) dict¶
- deletion(children: list) dict¶
- deletion_insertion(children: list) dict¶
- description(children: list) dict¶
- description_dna(children: list) dict¶
- description_protein(children: list) dict¶
- duplication(children: list) dict¶
- equal(children: list) dict¶
- exact_range(children: list) dict¶
- extension(children: list) dict¶
- frame_shift(children: list) dict¶
- insert(children: list) dict¶
- inserted(children: list) dict¶
- insertion(children: list) dict¶
- inversion(children: list) dict¶
- length(children: list) dict¶
- location(children: list) dict¶
- point(children: list) dict¶
- range(children: list) dict¶
- reference(children: list) dict¶
- repeat(children: list) dict¶
- repeat_mixed(children: list) dict¶
- repeat_number(children: list) dict¶
- substitution(children: list) dict¶
- uncertain_point(children: list) dict¶
- variant(children: list) dict¶
- variant_certain(children: list) dict¶
- variant_predicted(children: list) dict¶
- variants(children: list) dict¶
- variants_predicted(children: list) dict¶
- mutalyzer_hgvs_parser.convert.parse_tree_to_model(parse_tree: Tree) dict¶
Convert a parse tree to a nested dictionary model.
- Parameters:
parse_tree (lark.Tree) – HGVS description.
- Returns:
Description dictionary model.
- Return type:
dict
- mutalyzer_hgvs_parser.convert.to_model(description: str, start_rule: str | None = None) dict¶
Convert an HGVS description, or parts of it, e.g., a location, a variants list, etc., if an appropriate alternative start_rule is provided, to a nested dictionary model.
- Parameters:
description (str) – HGVS description.
start_rule (str) – Alternative start rule.
- Returns:
Description dictionary model.
- Return type:
dict