dandelion.preprocessing.external.tigger_genotype¶
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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.