orthomap.ncbitax module

Author: Kristian K Ullrich date: April 2023 email: ullrich@evolbio.mpg.de License: GPL-3

orthomap.ncbitax.add_argparse_args(parser: ArgumentParser)

This function attaches individual argument specifications to the parser.

Parameters:

parser (argparse.ArgumentParser) – An argparse.ArgumentParser.

orthomap.ncbitax.define_parser()

A helper function for using ncbitax.py via the terminal.

Returns:

An argparse.ArgumentParser.

Return type:

argparse.ArgumentParser

orthomap.ncbitax.main()

The main function that is being called when ncbitax.py is used via the terminal.

orthomap.ncbitax.update_ncbi()

This function updates or downloads the NCBI taxonomy database using the package ete3. A parsed version of it will be stored at the home directory: ~/.etetoolkit/taxa.sqlite.

Example

>>> from orthomap import ncbitax
>>> ncbitax.update_ncbi()