immuneML.IO package

Subpackages

• immuneML.IO.dataset_export package
  • Submodules
  • immuneML.IO.dataset_export.AIRRExporter module
    • AIRRExporter
      • AIRRExporter.export()
      • AIRRExporter.export_repertoire()
      • AIRRExporter.export_updated_metadata()
      • AIRRExporter.get_sequence_aa_field()
      • AIRRExporter.get_sequence_field()
      • AIRRExporter.update_gene_columns()
  • immuneML.IO.dataset_export.DataExporter module
    • DataExporter
      • DataExporter.export()
  • immuneML.IO.dataset_export.ImmuneMLExporter module
    • ImmuneMLExporter
      • ImmuneMLExporter.export()
  • Module contents
• immuneML.IO.dataset_import package
  • Submodules
  • immuneML.IO.dataset_import.AIRRImport module
    • AIRRImport
      • AIRRImport.alternative_load_func()
      • AIRRImport.get_documentation()
      • AIRRImport.import_dataset()
      • AIRRImport.import_receptors()
      • AIRRImport.preprocess_dataframe()
  • immuneML.IO.dataset_import.DataImport module
    • DataImport
      • DataImport.import_dataset()
  • immuneML.IO.dataset_import.DatasetImportParams module
    • DatasetImportParams
      • DatasetImportParams.build_object()
      • DatasetImportParams.column_mapping
      • DatasetImportParams.column_mapping_synonyms
      • DatasetImportParams.columns_to_load
      • DatasetImportParams.import_empty_aa_sequences
      • DatasetImportParams.import_empty_nt_sequences
      • DatasetImportParams.import_illegal_characters
      • DatasetImportParams.import_out_of_frame
      • DatasetImportParams.import_productive
      • DatasetImportParams.import_unproductive
      • DatasetImportParams.import_with_stop_codon
      • DatasetImportParams.is_repertoire
      • DatasetImportParams.metadata_column_mapping
      • 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()
      • GenericImport.import_dataset()
      • GenericImport.import_receptors()
      • GenericImport.preprocess_dataframe()
  • immuneML.IO.dataset_import.IGoRImport module
    • IGoRImport
      • IGoRImport.CODON_TABLE
      • IGoRImport.get_documentation()
      • IGoRImport.import_dataset()
      • IGoRImport.preprocess_dataframe()
      • IGoRImport.translate_sequence()
  • immuneML.IO.dataset_import.IReceptorImport module
    • IReceptorImport
      • IReceptorImport.REPERTOIRES_FOLDER
      • IReceptorImport.get_documentation()
      • IReceptorImport.import_dataset()
      • IReceptorImport.import_repertoire_dataset()
      • IReceptorImport.import_sequence_dataset()
  • immuneML.IO.dataset_import.ImmuneMLImport module
    • ImmuneMLImport
      • ImmuneMLImport.import_dataset()
  • immuneML.IO.dataset_import.ImmunoSEQRearrangementImport module
    • ImmunoSEQRearrangementImport
      • ImmunoSEQRearrangementImport.get_documentation()
      • ImmunoSEQRearrangementImport.import_dataset()
      • ImmunoSEQRearrangementImport.preprocess_dataframe()
  • immuneML.IO.dataset_import.ImmunoSEQSampleImport module
    • ImmunoSEQSampleImport
      • ImmunoSEQSampleImport.get_documentation()
      • ImmunoSEQSampleImport.import_dataset()
      • ImmunoSEQSampleImport.preprocess_dataframe()
  • immuneML.IO.dataset_import.MiXCRImport module
    • MiXCRImport
      • MiXCRImport.SEQUENCE_NAME_MAP
      • MiXCRImport.get_documentation()
      • MiXCRImport.import_dataset()
      • MiXCRImport.preprocess_dataframe()
  • immuneML.IO.dataset_import.OLGAImport module
    • OLGAImport
      • OLGAImport.alternative_load_func()
      • OLGAImport.get_documentation()
      • OLGAImport.import_dataset()
      • OLGAImport.preprocess_dataframe()
  • 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.SingleLineReceptorImport module
    • SingleLineReceptorImport
      • SingleLineReceptorImport.get_documentation()
      • SingleLineReceptorImport.import_dataset()
      • SingleLineReceptorImport.make_gene_columns()
  • immuneML.IO.dataset_import.TenxGenomicsImport module
    • TenxGenomicsImport
      • TenxGenomicsImport.get_documentation()
      • TenxGenomicsImport.import_dataset()
      • TenxGenomicsImport.import_receptors()
      • TenxGenomicsImport.preprocess_dataframe()
  • immuneML.IO.dataset_import.VDJdbImport module
    • VDJdbImport
      • VDJdbImport.KEY_MAPPING
      • VDJdbImport.extract_meta_columns()
      • VDJdbImport.get_documentation()
      • VDJdbImport.get_sequence_identifiers()
      • VDJdbImport.import_dataset()
      • VDJdbImport.import_receptors()
      • VDJdbImport.preprocess_dataframe()
  • 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