immuneML.dsl.definition_parsers package

Submodules

immuneML.dsl.definition_parsers.DefinitionParser module

class immuneML.dsl.definition_parsers.DefinitionParser.DefinitionParser[source]

Bases: object

static generate_docs(path: Path)[source]
static make_dataset_docs(path: Path)[source]
static make_encodings_docs(path: Path)[source]
static make_ml_methods_docs(path: Path)[source]
static make_preprocessing_docs(path: Path)[source]
static make_reports_docs(path: Path)[source]
static make_simulation_docs(path: Path)[source]
static parse(workflow_specification: dict, symbol_table: SymbolTable, result_path: Path)[source]

immuneML.dsl.definition_parsers.DefinitionParserOutput module

class immuneML.dsl.definition_parsers.DefinitionParserOutput.DefinitionParserOutput(symbol_table: SymbolTable, specification: dict)[source]

Bases: object

immuneML.dsl.definition_parsers.EncodingParser module

class immuneML.dsl.definition_parsers.EncodingParser.EncodingParser[source]

Bases: object

keyword = 'encodings'
static parse(encodings: dict, symbol_table: SymbolTable)[source]
static parse_encoder(*args, **kwargs)

immuneML.dsl.definition_parsers.MLParser module

class immuneML.dsl.definition_parsers.MLParser.MLParser[source]

Bases: object

static create_method_instance(ml_specification: dict, ml_method_class, key: str) → tuple[source]
keyword = 'ml_methods'
static parse(specification: dict, symbol_table: SymbolTable)[source]
static parse_any_model(ml_method_id, ml_specification, ml_class_name)[source]
static parse_by_type(ml_method_id, ml_specification, valid_class_values)[source]
static parse_classifiers(ml_method_id, ml_specification, ml_class_name)[source]

immuneML.dsl.definition_parsers.MotifParser module

class immuneML.dsl.definition_parsers.MotifParser.MotifParser[source]

Bases: object

keyword = 'motifs'
static parse(motifs: dict, symbol_table: SymbolTable)[source]

immuneML.dsl.definition_parsers.PreprocessingParser module

class immuneML.dsl.definition_parsers.PreprocessingParser.PreprocessingParser[source]

Bases: object

keyword = 'preprocessing_sequences'
static parse(specs: dict, symbol_table: SymbolTable)[source]

immuneML.dsl.definition_parsers.ReportParser module

class immuneML.dsl.definition_parsers.ReportParser.ReportParser[source]

Bases: object

keyword = 'reports'
static parse(reports: dict, symbol_table: SymbolTable)[source]

immuneML.dsl.definition_parsers.SignalParser module

class immuneML.dsl.definition_parsers.SignalParser.SignalParser[source]

Bases: object

custom_func_keys = ['source_file', 'is_present_func']
keyword = 'signals'
static parse(*args, **kwargs)
immuneML.dsl.definition_parsers.SignalParser.check_clonal_frequency(spec: dict, name: str = 'clonal_frequency', location: str = 'SignalParser')[source]

immuneML.dsl.definition_parsers.SimulationParser module

class immuneML.dsl.definition_parsers.SimulationParser.SimulationParser[source]

Bases: object

keyword = 'simulations'
static parse(simulations: dict, symbol_table: SymbolTable)[source]
immuneML.dsl.definition_parsers.SimulationParser.check_sim_strategy_setup(simulation: dict)[source]
immuneML.dsl.definition_parsers.SimulationParser.strategy_supports_signals(sim_item, sim_strategy_cls)[source]

Module contents