immuneML.IO package

Subpackages

• immuneML.IO.dataset_export package
  • Submodules
  • immuneML.IO.dataset_export.AIRRExporter module
    • AIRRExporter
      • AIRRExporter.add_cdr3_from_junction()
      • AIRRExporter.export()
      • AIRRExporter.export_repertoire_dataset()
      • AIRRExporter.export_repertoire_files()
      • AIRRExporter.process_and_store_data_file()
      • AIRRExporter.process_and_store_dataset_file()
  • immuneML.IO.dataset_export.DataExporter module
    • DataExporter
      • DataExporter.export()
  • Module contents
• immuneML.IO.dataset_import package
  • Submodules
  • immuneML.IO.dataset_import.AIRRImport module
    • AIRRImport
      • AIRRImport.get_documentation()
  • immuneML.IO.dataset_import.DataImport module
    • DataImport
      • DataImport.determine_repertoire_dataset_labels()
      • DataImport.determine_repertoire_type_dict()
      • DataImport.import_dataset()
      • DataImport.import_dataset_from_yaml()
      • DataImport.import_element_dataset()
      • DataImport.import_receptor_dataset()
      • DataImport.import_repertoire_dataset()
      • DataImport.import_repertoire_metadata()
      • DataImport.import_sequence_dataset()
      • DataImport.load_file()
      • DataImport.load_repertoire_object()
      • DataImport.load_repertoires()
      • DataImport.load_sequence_dataframe()
      • DataImport.preprocess_file()
  • immuneML.IO.dataset_import.DatasetImportParams module
    • DatasetImportParams
      • DatasetImportParams.build_object()
      • DatasetImportParams.column_mapping
      • DatasetImportParams.column_mapping_synonyms
      • DatasetImportParams.columns_to_load
      • DatasetImportParams.dataset_file
      • DatasetImportParams.import_empty_aa_sequences
      • DatasetImportParams.import_empty_nt_sequences
      • DatasetImportParams.import_illegal_characters
      • DatasetImportParams.import_out_of_frame
      • DatasetImportParams.import_productive
      • DatasetImportParams.import_unknown_productivity
      • DatasetImportParams.import_unproductive
      • DatasetImportParams.import_with_stop_codon
      • DatasetImportParams.is_repertoire
      • DatasetImportParams.label_columns
      • DatasetImportParams.metadata_file
      • DatasetImportParams.number_of_processes
      • DatasetImportParams.organism
      • DatasetImportParams.paired
      • DatasetImportParams.path
      • DatasetImportParams.receptor_chains
      • DatasetImportParams.region_type
      • DatasetImportParams.result_path
      • DatasetImportParams.separator
      • DatasetImportParams.sequence_file_size
  • immuneML.IO.dataset_import.GenericImport module
    • GenericImport
      • GenericImport.get_documentation()
  • immuneML.IO.dataset_import.IGoRImport module
    • IGoRImport
      • IGoRImport.CODON_TABLE
      • IGoRImport.get_documentation()
      • IGoRImport.preprocess_file()
      • IGoRImport.translate_sequence()
  • immuneML.IO.dataset_import.IReceptorImport module
    • IReceptorImport
      • IReceptorImport.REPERTOIRES_FOLDER
      • IReceptorImport.get_documentation()
      • IReceptorImport.import_repertoire_dataset()
      • IReceptorImport.import_sequence_dataset()
  • immuneML.IO.dataset_import.ImmunoSEQRearrangementImport module
    • ImmunoSEQRearrangementImport
      • ImmunoSEQRearrangementImport.get_documentation()
      • ImmunoSEQRearrangementImport.preprocess_file()
  • immuneML.IO.dataset_import.ImmunoSEQSampleImport module
    • ImmunoSEQSampleImport
      • ImmunoSEQSampleImport.get_documentation()
      • ImmunoSEQSampleImport.preprocess_file()
  • immuneML.IO.dataset_import.MiXCRImport module
    • MiXCRImport
      • MiXCRImport.get_documentation()
      • MiXCRImport.preprocess_file()
    • load_alleles()
  • immuneML.IO.dataset_import.OLGAImport module
    • OLGAImport
      • OLGAImport.get_documentation()
      • OLGAImport.load_file()
  • immuneML.IO.dataset_import.RandomReceptorDatasetImport module
    • RandomReceptorDatasetImport
      • RandomReceptorDatasetImport.import_dataset()
  • immuneML.IO.dataset_import.RandomRepertoireDatasetImport module
    • RandomRepertoireDatasetImport
      • RandomRepertoireDatasetImport.import_dataset()
  • immuneML.IO.dataset_import.RandomSequenceDatasetImport module
    • RandomSequenceDatasetImport
      • RandomSequenceDatasetImport.import_dataset()
  • immuneML.IO.dataset_import.TenxGenomicsImport module
    • TenxGenomicsImport
      • TenxGenomicsImport.get_documentation()
  • immuneML.IO.dataset_import.VDJdbImport module
    • VDJdbImport
      • VDJdbImport.KEY_MAPPING
      • VDJdbImport.extract_dict_columns()
      • VDJdbImport.get_documentation()
      • VDJdbImport.get_sequence_identifiers()
      • VDJdbImport.preprocess_file()
  • Module contents
• immuneML.IO.ml_method package
  • Submodules
  • immuneML.IO.ml_method.MLExporter module
    • MLExporter
      • MLExporter.export()
      • MLExporter.export_zip()
  • immuneML.IO.ml_method.MLImport module
    • MLImport
      • MLImport.import_encoder()
      • MLImport.import_hp_setting()
      • MLImport.import_label()
      • MLImport.import_preprocessing_sequence()
  • immuneML.IO.ml_method.MLMethodConfiguration module
    • MLMethodConfiguration
      • MLMethodConfiguration.encoding_class
      • MLMethodConfiguration.encoding_file
      • MLMethodConfiguration.encoding_name
      • MLMethodConfiguration.encoding_parameters
      • MLMethodConfiguration.label_name
      • MLMethodConfiguration.label_positive_class
      • MLMethodConfiguration.label_values
      • MLMethodConfiguration.load()
      • MLMethodConfiguration.ml_method
      • MLMethodConfiguration.ml_method_name
      • MLMethodConfiguration.preprocessing_file
      • MLMethodConfiguration.preprocessing_parameters
      • MLMethodConfiguration.preprocessing_sequence_name
      • MLMethodConfiguration.software_used
      • MLMethodConfiguration.store()
      • MLMethodConfiguration.train_dataset_id
      • MLMethodConfiguration.train_dataset_name
  • immuneML.IO.ml_method.UtilIO module
    • UtilIO
      • UtilIO.export_comparison_data()
      • UtilIO.export_pairwise_comparison()
      • UtilIO.import_comparison_data()
      • UtilIO.import_pairwise_comparison()
  • Module contents

Module contents