dandelion.preprocessing.reannotate_genes

dandelion.preprocessing.reannotate_genes(data, igblast_db=None, germline=None, org='human', loci='ig', extended=True, verbose=False)[source]

Reannotate cellranger fasta files with igblastn and parses to airr/changeo data format.

Parameters
  • data (Sequence) – list of fasta file locations, or folder name containing fasta files. if provided as a single string, it will first be converted to a list; this allows for the function to be run on single/multiple samples.

  • igblast_db (str, PathLike, optional) – path to igblast database folder. Defaults to $IGDATA environmental variable.

  • germline (str, PathLike, optional) – path to germline database folder. Defaults to $GERMLINE environmental variable.

  • org (str) – organism of germline database. Default is ‘human’.

  • loci (str) – mode for igblastn. Default is ‘ig’ for BCRs. Also accepts ‘tr’ for TCRs.

  • extended (bool) – whether or not to transfer additional 10X annotions to output file. Default is True.

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

Returns

Return type

V(D)J data file in airr/changeo data format.