dandelion.polars.core.Dandelion.store_germline_reference

Dandelion.store_germline_reference(corrected=None, germline=None, org='human', db='imgt')

Update germline reference with corrected sequences and store in Dandelion object.

Parameters:

  • corrected (dict[str, str] | str | None, optional) – dictionary of corrected germline sequences or file path to corrected germline sequences fasta file.

  • germline (str | None, optional) – path to germline database folder. Defaults to `` environmental variable.

  • org (Literal[“human”, “mouse”], optional) – organism of reference folder. Default is ‘human’.

  • db (Literal[“imgt”, “ogrdb”], optional) – database of reference sequences. Default is ‘imgt’.

Raises:

  • KeyError – if GERMLINE environmental variable is not set.

  • TypeError – if incorrect germline provided.

Return type:

None