ExperimentalImport

Allows to import existing experimental data and perform annotations and simulations on top of them.

Arguments:

  • import_format (str): see the list of supported formats under Supported dataset formats

  • tmp_import_path (str): where to store the imported files

  • import_params (dict): as defined under the import format selected in the first parameter; for details see Supported dataset formats

YAML specification:

generative_model:
    import_format: AIRR
    tmp_import_path: ./tmp/
    import_params:
        path: path/to/files/
        region_type: IMGT_CDR3 # what part of the sequence to import
        column_mapping: # column mapping AIRR: ligo
            junction: sequence
            junction_aa: sequence_aa
            locus: chain
    type: ExperimentalImport

OLGA

This is a wrapper for the OLGA package as described by Sethna et al. 2019 (OLGA package on PyPI or GitHub: https://github.com/statbiophys/OLGA).

Reference:

Zachary Sethna, Yuval Elhanati, Curtis G Callan, Jr, Aleksandra M Walczak, Thierry Mora, OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs, Bioinformatics, Volume 35, Issue 17, 1 September 2019, Pages 2974–2981, https://doi.org/10.1093/bioinformatics/btz035

Note:

  • OLGA generates sequences that correspond to IMGT junction and are used for matching as such. See the https://github.com/statbiophys/OLGA for more details.

  • Gene names are as provided in OLGA (either in default models or in the user-specified model files). For simulation, one should use gene names in the same format.

Arguments:

  • model_path (str): if not default model, this parameter should point to a folder where the four OLGA/IGOR format files are stored (could also be inferred from some experimental data)

  • default_model_name (str): if not using custom models, one of the OLGA default models could be specified here; the value should be the same as it would be passed to command line in OLGA: e.g., humanTRB, human IGH

YAML specification:

generative_model:
    type: OLGA
    model_path: None
    default_model_name: humanTRB