dandelion.base.preprocessing.annotate_functionality

dandelion.base.preprocessing.annotate_functionality(vdj, germline=None, org='human', db='imgt')[source]

Annotate V/D/J gene functionality from germline reference FASTA headers.

Parameters:

  • vdj (Dandelion) – Dandelion object containing AIRR-style calls in .data.

  • germline (Path | str | None, optional) – Path to germline database root, db/org, or db/org/vdj. If None, resolves from the GERMLINE environment variable using IMGT defaults for the selected organism.

  • org (Literal[“human”, “mouse”], optional) – Organism used when resolving default/reference directory layout.

  • db (Literal[“imgt”, “ogrdb”, “kiarva”, “gkhlab”], optional) – Database to use. Defaults to “imgt”.

Returns:

The same vdj object with additional columns: v_call_functionality, d_call_functionality, and j_call_functionality.

Return type:

Dandelion