app API reference

taxadb2.app.create_db(args)

Main function for the ‘taxadb create’ sub-command.

This function creates a taxonomy database with 3 tables: Taxa, Sequence and DeprecatedTaxID.

Parameters:

args.input (str) – input directory. It is the directory created by taxadb download
args.dbname (str) – name of the database to be created
args.dbtype (str) – type of database to be used.
args.division (str) – division to create the db for.
args.fast (bool) – Disables checks for faster db creation. Use with caution!

taxadb2.app.download_files(args)

Main function for the taxadb download sub-command.

This function can download taxump.tar.gz and the content of the accession2taxid directory from the ncbi ftp.