pyphy 1.0.4

A python package to interact with NCBI taxonomy

pyphy

Python library that interacts with NCBI taxonomy

This is the Python implementation of the blog post http://dgg32.blogspot.com/2013/07/pyphy-wrapper-program-for-ncbi-sqlite.html.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

sqlite

Preparing the backend database

Notice: please perform this step periodically to stay up to date with the NCBI Taxonomy.

Download the taxdmp.zip from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/ and unzip it.

python prepyphy.py [ncbi_download_folder] [db_path]

This step will set up the "db_path" in pyphy.config automatically.

If you move the database afterwards, please don't forget to refresh db_path in pyphy.config.

Using the library

Install the library via pip

pip install pyphy

Then you can import the pyphy library in your Python code by

import pyphy

pyphy provides the following queries inside the NCBI taxonomy:

Taxonomy name <-> NCBI TaxID

NCBI TaxID -> Full lineage

NCBI TaxID -> Taxonomic rank

NCBI TaxID -> all children

For code examples and documentation please refer to documentations.

Authors

• Sixing Huang - Concept and Coding

License

This project is licensed under the MIT License - see the LICENSE file for details