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 :ref:`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 :ref:`Supported dataset formats`

YAML specification:

.. indent with spaces
.. code-block:: yaml

    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:

.. indent with spaces
.. code-block:: yaml

    generative_model:
        type: OLGA
        model_path: None
        default_model_name: humanTRB