dandelion.preprocessing.external.tigger_genotype

dandelion.preprocessing.external.tigger_genotype(data, v_germline=None, outdir=None, org='human', fileformat='airr', novel_='YES', verbose=False)[source]

Reassign alleles with TIgGER in R.

Parameters
  • data (PathLike) – vdj tabulated data, in Change-O (TAB) or AIRR (TSV) format.

  • germline (PathLike, optional) – fasta file containing IMGT-gapped V segment reference germlines. Defaults to $GERMLINE.

  • outdir (PathLike, optional) – output directory. Will be created if it does not exist. Defaults to the current working directory.

  • org (str) – organism for germline sequences.

  • fileformat (str) – format for running tigger. Default is ‘airr’. Also accepts ‘changeo’.

  • novel (str) – whether or not to run novel allele discovery. Default is ‘YES’.

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