taxidTools: A Python Toolkit for Taxonomy

taxidTools is a Python library to handle Taxonomy definitions.

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Usage example:

>>> import taxidTools
>>> tax = taxidTools.Taxonomy.from_taxdump("nodes.dmp", "rankedlineage.dmp")
>>> tax.getName('9606')
'Homo sapiens'
>>> lineage = tax.getAncestry('9606')
>>> lineage.filter()
>>> [node.name for node in lineage]
['Homo sapiens', 'Homo', 'Hominidae', 'Primates', 'Mammalia', 'Chordata', 'Metazoa']
>>> tax.lca(['9606', '10090']).name
'Euarchontoglires'
>>> tax.distance('9606', '10090')
18

taxidTools allows you to easily handle complex taxonomies from different sources and perform common operations such as consensus determination, finding a last common ancestor or calculating node distances.

User Guide

Get it installed and jump right in:

• Installation guide
  • Using pip
  • Using conda
  • Development version
• Quickstart
  • Loading taxonomy information
  • Accessing node infos
  • Ancestries
• Advanced usage
  • A word of caution on mutable types
  • Consensus determination
  • Distances
  • Rerooting, filtering and normalizing taxonomies
  • Reading and writing taxonomies
  • Working with non-NCBI taxonomies

API Documentation

Source code documentation.

• Taxonomy module
• Lineage module
• Node module
• utils module

Cite us

If you are using taxidTools for your reasearch, cite the latest version from Zenodo.

Changes

• Release History
  • 2.2.3 (2021-10-08)
  • 2.2.2 (2021-09-21)
  • 2.2.0(2021-09-21)
  • 2.1.2 (2021-08-18)
  • 2.1.1 (2021-07-15)
  • 2.1.0 (2021-07-14)
  • 2.0.0 (2021-07-13)