https://github.com/cvua-rrw/taxidtools

Python library to deal with taxonomic IDs and lineages from the NCBI's Taxdump files
https://github.com/cvua-rrw/taxidtools

ancestry lineage lineages ncbi ncbi-taxonomy python python-library taxdump taxids taxonomy

Last synced: 4 months ago
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Python library to deal with taxonomic IDs and lineages from the NCBI's Taxdump files

• Host: GitHub
• URL: https://github.com/cvua-rrw/taxidtools
• Owner: CVUA-RRW
• License: bsd-3-clause
• Created: 2020-10-02T11:35:52.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2024-06-25T11:01:30.000Z (almost 2 years ago)
• Last Synced: 2025-10-21T20:08:01.228Z (8 months ago)
• Topics: ancestry, lineage, lineages, ncbi, ncbi-taxonomy, python, python-library, taxdump, taxids, taxonomy
• Language: Python
• Homepage: https://cvua-rrw.github.io/taxidtools/
• Size: 1.01 MB
• Stars: 2
• Watchers: 0
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • Changelog: HISTORY.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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# TaxidTools - A Python Toolkit for Taxonomy

**taxidTools** is a Python library to handle Taxonomy definitions.

## Highlights

* Load taxonomy defintions for the NCBI's taxdump files

* Prune, filter, and normalize branches

* Save as JSON for later use

* Determine consensus, last common ancestor, or distances

* Retrieve ancestries or list descendants

* Export as Newick trees

## Installation

With `pip`:

```bash

pip install taxidtools

```

With `conda`:

```bash

conda install -c conda-forge taxidtools

```

With `docker`:

```bash

docker pull gregdenay/taxidtools

```

## Quickstart

With the [NCBI's taxdump files](https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/) installed locally:

```python

>>> import taxidTools

>>> tax = taxidTools.read_taxdump('nodes.dmp', 'rankedlineage.dmp', 'merged.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

```

## Documentation

Full documentation is hosted on the [homepage](https://cvua-rrw.github.io/taxidtools/)

## Cite us

If you use taxidTools for your reasearch, you can cite it using the 

DOI at the top of this page.