dandelion.base.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