dandelion.preprocessing.external.creategermlines

dandelion.preprocessing.external.creategermlines(db_file, germtypes=None, germline=None, org='human', genotype_fasta=None, v_field=None, cloned=False, mode=None, verbose=False)[source]

Wrapper for CreateGermlines.py for reconstructing germline sequences,

Parameters
  • db_file (PathLike) – path to AIRR table.

  • germtypes (str, optional) – germline type for reconstuction.

  • germline (PathLike, optional) – location to germline fasta files.

  • org (str) – organism for germline sequences.

  • genotype_fasta (PathLike, optional) – location to corrected v germine fasta file.

  • v_field (str, optional) – name of column for v segment to perform reconstruction.

  • cloned (bool) – whether or not to run with cloned option.

  • mode (str, optional) – whether to run on heavy or light mode. If left as None, heavy and light will be run together.

  • verbose (bool) – whether or not to print the command used in terminal. Default is False.