dandelion.external.immcantation.base.changeo.makedb_igblast

dandelion.external.immcantation.base.changeo.makedb_igblast(fasta, igblast_output=None, germline=None, org='human', db='imgt', extended=True, additional_args=[], loci='ig')[source]

Parse IgBLAST output to AIRR format.

Parameters:

  • fasta (Path | str) – path to fasta file used for reannotation.

  • igblast_output (Path | str | None, optional) – path to igblast output file.

  • germline (str | None, optional) – path to germline database.

  • org (Literal[“human”, “mouse”], optional) – organism of germline sequences.

  • db (Literal[“imgt”, “ogrdb”], optional) – imgt or ogrdb reference database for running igblastn.

  • extended (bool, optional) – whether or not to parse extended 10x annotations.

  • additional_args (list[str], optional) – Additional arguments to pass to MakeDb.py.