Metadata-Version: 2.1
Name: living-tree
Version: 0.0.6
Summary: An efficient toolkit for constructing and processing taxonomic trees (metagenomic reads count, remapping, etc.).
Home-page: https://github.com/AdeBC/living-tree-toolkit
Author: Hui Chong
Author-email: huichong.me@gmail.com
License: MIT
Keywords: taxonomic tree,living tree,tree data processing
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Programming Language :: Python :: 3.7
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
License-File: LICENSE

# living-tree-toolkit

An efficient toolkit for processing taxonomic trees (abundance calculations, reads count statistics, etc.)  and generating taxonomic trees using lineages data retrieved from the NCBI taxonomy database.

![Status Beta](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square&logo=appveyor)
[![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square&logo=appveyor)](http://makeapullrequest.com)
[![Read the Docs (version)](https://img.shields.io/readthedocs/living-tree-toolkit/latest?label=documentation&style=flat-square)](https://living-tree-toolkit.readthedocs.io/en/latest/)


Use [`treelib`](https://github.com/caesar0301/treelib) API to achieve rapid construction of complex trees and [`ete3 toolkit`](http://etetoolkit.org/) API to retrieve data from NCBI taxonomy database.

This project is a sub-project of the ONN4MDM project, if you use it for academic purposes, please cite us.

## Update

- 2020/03/27:  
    - start finalizing project framework and release initial version.
- 2020/04/14:  
    - Api update `update_value` and `get_matrix`
    - New method `get_top_down_ids`, `get_bottom_up_ids`, `get_ids_by_level` and `get_paths_to_level`
    - Execution efficiency are improved significantly
    
## Documentation

For Installation, examples and API references, see [https://living-tree-toolkit.readthedocs.io/en/latest/](https://living-tree-toolkit.readthedocs.io/en/latest/)

## Maintainer

| Name      | Email                   | Organization                                                 |
| --------- | ----------------------- | ------------------------------------------------------------ |
| Hui Chong | huichong.me@gmail.com | Research Assistant, Institute of Science and Technology for Brain-inspired Intelligence, Fudan University |



