app API reference

taxadb.app.create_db(args)

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

This function creates a taxonomy database with 2 tables: Taxa and Sequence.

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!

taxadb.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.

Parameters:args (object) – The arguments from argparse