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: lark.visitors.Transformer

AA(name)

COORDINATE_SYSTEM(name)

ID(name)

INVERTED(name)

OFFSET(name)

OUTSIDE_CDS(name)

P_SEQUENCE(name)

SEQUENCE(name)

UNKNOWN(name)

conversion(children)

deletion(children)

deletion_insertion(children)

description(children)

description_dna(children)

description_protein(children)

duplication(children)

equal(children)

exact_range(children)

extension(children)

frame_shift(children)

insert(children)

inserted(children)

insertion(children)

inversion(children)

length(children)

location(children)

point(children)

range(children)

reference(children)

repeat(children)

repeat_mixed(children)

repeat_number(children)

substitution(children)

uncertain_point(children)

variant(children)

variant_certain(children)

variant_predicted(children)

variants(children)

variants_predicted(children)

mutalyzer_hgvs_parser.convert.parse_tree_to_model(parse_tree)

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, start_rule=None)

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