pyphy 1.0.3

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

In order to use the library system wide, add this line to your ~/.bashrc.

export PYTHONPATH="${PYTHONPATH}:/my/own/pyphy/source/"

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