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License](https://img.shields.io/pypi/l/Django?style=flat)](LICENSE)\n[![GitHub release (latest by date)](https://img.shields.io/github/v/release/CVUA-RRW/taxidTools?logo=GitHub)](https://github.com/CVUA-RRW/taxidtools/releases)\n[![Conda Version](https://img.shields.io/conda/vn/conda-forge/taxidtools.svg?logo=Conda-Forge)](https://anaconda.org/conda-forge/taxidtools)\n[![Pypi Version](https://img.shields.io/pypi/v/taxidTools?style=flat?logo=pypi)](https://pypi.org/project/taxidTools/)\n[![Docker Image Version](https://img.shields.io/docker/v/gregdenay/taxidtools?logo=Docker\u0026label=DockerHub)](https://hub.docker.com/r/gregdenay/taxidtools/tags)\n[![DOI](https://zenodo.org/badge/300595196.svg)](https://zenodo.org/doi/10.5281/zenodo.5094583)\n\n# TaxidTools - A Python Toolkit for Taxonomy\n\n**taxidTools** is a Python library to handle Taxonomy definitions.\n\n## Highlights\n\n* Load taxonomy defintions for the NCBI's taxdump files\n* Prune, filter, and normalize branches\n* Save as JSON for later use\n* Determine consensus, last common ancestor, or distances\n* Retrieve ancestries or list descendants\n* Export as Newick trees\n\n## Installation\n\nWith `pip`:\n\n```bash\npip install taxidtools\n```\n\nWith `conda`:\n\n```bash\nconda install -c conda-forge taxidtools\n```\n\nWith `docker`:\n\n```bash\ndocker pull gregdenay/taxidtools\n```\n\n## Quickstart\n\nWith the [NCBI's taxdump files](https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/) installed locally:\n\n```python\n\u003e\u003e\u003e import taxidTools\n\u003e\u003e\u003e tax = taxidTools.read_taxdump('nodes.dmp', 'rankedlineage.dmp', 'merged.dmp')\n\u003e\u003e\u003e tax.getName('9606')\n'Homo sapiens'\n\u003e\u003e\u003e lineage = tax.getAncestry('9606')\n\u003e\u003e\u003e lineage.filter()\n\u003e\u003e\u003e [node.name for node in lineage]\n['Homo sapiens', 'Homo', 'Hominidae', 'Primates', 'Mammalia', 'Chordata', 'Metazoa']\n\u003e\u003e\u003e tax.lca(['9606', '10090']).name\n'Euarchontoglires'\n\u003e\u003e\u003e tax.distance('9606', '10090')\n18\n```\n\n## Documentation\n\nFull documentation is hosted on the [homepage](https://cvua-rrw.github.io/taxidtools/)\n\n## Cite us\n\nIf you use taxidTools for your reasearch, you can cite it using the \nDOI at the top of this page.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcvua-rrw%2Ftaxidtools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcvua-rrw%2Ftaxidtools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcvua-rrw%2Ftaxidtools/lists"}