immuneML.dsl.instruction_parsers package

Submodules

immuneML.dsl.instruction_parsers.ApplyGenModelParser module

immuneML.dsl.instruction_parsers.ClusteringParser module

immuneML.dsl.instruction_parsers.DatasetExportParser module

class immuneML.dsl.instruction_parsers.DatasetExportParser.DatasetExportParser[source]

Bases: object

Specification of instruction with a random datasets:

definitions:
datasets:
my_generated_dataset: # a dataset to be exported in the given format

format: RandomRepertoireDataset params:

result_path: generated_dataset/ repertoire_count: 100 sequence_count_probabilities:

100: 0.5 120: 0.5

sequence_length_probabilities:

12: 0.333 13: 0.333 14: 0.333

labels:
immune_event_1:

yes: 0.5 no: 0.5

preprocessing_sequences:
my_preprocessing:
  • my_filter:
    ClonesPerRepertoireFilter:

    lower_limit: 110 upper_limit: 200

instructions:
my_instruction1: # instruction name

type: DatasetExport datasets: # list of datasets to export

  • my_generated_dataset

preprocessing_sequence: my_preprocessing_sequence number_of_processes: 4 export_formats: # list of formats to export the datasets to

  • AIRR

OPTIONAL_KEYS = ['preprocessing_sequence', 'number_of_processes']
REQUIRED_KEYS = ['type', 'datasets', 'export_formats']
parse(key: str, instruction: dict, symbol_table: SymbolTable, path: Path = None) → DatasetExportInstruction[source]

immuneML.dsl.instruction_parsers.ExploratoryAnalysisParser module

immuneML.dsl.instruction_parsers.FeasibilitySummaryParser module

immuneML.dsl.instruction_parsers.LabelHelper module

class immuneML.dsl.instruction_parsers.LabelHelper.LabelHelper[source]

Bases: object

static check_label_format(labels: list, instruction_name: str, yaml_location: str)[source]
static create_label_config(labels: list, dataset: Dataset, instruction_name: str, yaml_location: str) → LabelConfiguration[source]

immuneML.dsl.instruction_parsers.LigoSimParser module

immuneML.dsl.instruction_parsers.MLApplicationParser module

immuneML.dsl.instruction_parsers.SubsamplingParser module

class immuneML.dsl.instruction_parsers.SubsamplingParser.SubsamplingParser[source]

Bases: object

parse(key: str, instruction: dict, symbol_table: SymbolTable, path: Path = None) → SubsamplingInstruction[source]

immuneML.dsl.instruction_parsers.TrainGenModelParser module

immuneML.dsl.instruction_parsers.TrainMLModelParser module

Module contents