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.