gene.etl.ncbi#

Defines ETL methods for the NCBI data source.

class gene.etl.ncbi.NCBI(database, seqrepo_dir=SEQREPO_ROOT_DIR, data_path=None, silent=True)[source]#

ETL class for NCBI source

__init__(database, seqrepo_dir=SEQREPO_ROOT_DIR, data_path=None, silent=True)[source]#

Instantiate Base class.

Parameters:

  • database (AbstractDatabase) – database instance

  • seqrepo_dir (Path) – Path to seqrepo directory

  • data_path (Optional[Path]) – path to app data directory

  • silent (bool) – if True, don’t print ETL result to console