bactax 0.2.0

A simple python tool for getting bacterial taxonomy and gram stain information from NCBI taxonomy data.

Installation

The most recently released version of bactax can be downloaded with pip:

pip install bactax

Usage

Getting taxonomic information for a bacteria

import bactax

genus = "akkermansia"
taxonomy = bactax.get_taxonomy(genus=genus) # returns a Taxonomy object

This will return a Taxonomy object with all the information above the level of genus filled in (i.e., family, order, class, etc.).

Determining gram stain

import bactax

genus = "escherichia"
gram_stain = bactax.gram_stain(genus=genus) # returns Gram.NEGATIVE

Updating the taxonomy data

bactax uses data from NCBI's taxonomy database. This data is downloaded and stored in a gzipped csv within the package. Since NCBI regularly updates their data, bactax provides a method to download the latest taxonomy database from NCBI.

import bactax
bactax.update()