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.