Taxadb2

Taxadb2 is an application to locally query the ncbi taxonomy.

taxadb2

Taxadb2 is a fork from taxadb original developed by Hadrien Gourlé and colleagues.

Taxadb2 handles the merged.dmp ncbi taxonomy file to deal with updated taxIDs.

Taxadb2 is written in python, and access its database using the peewee library.

In brief Taxadb2:

• is a small tool to query the ncbi taxonomy.

• is written in python >= 3.10.

• has built-in support for SQLite, MySQL and PostgreSQL.

• has available pre-built SQLite databases (Download build databases).

• has a comprehensive API documentation.

• is actively being developed on GitHub and available under the MIT license. Please see the README for more information on development, support, and contributing.

Quickstart

Click on the images below to access the documentation for creating the database with the engine you wish to use:

• Installation guide explains how to install Taxadb2.

• Download or build data explains how to build Taxadb2 database(s).

• Test the application allows to run several tests for supported databases.

• Querying taxadb shows examples on how to query a Taxadb database.

• API reference describes available classes and methods to use Taxadb.

Contents

• Installing Taxadb2
  • Using pip
  • From github
• Create a database
  • Build you own database
• Testing Taxadb
  • Running tests against PostgreSQL or MySQL
• Querying the database
  • taxids
  • accession numbers
  • Using configuration file or environment variable
• API Documentation
  • accessionid API reference
  • app API reference
  • parser API reference
  • taxadb2 API reference
  • taxaid API reference
  • schema API reference
  • util API reference

Indices and tables

• Index

• Module Index

• Search Page

This documentation was generated on 2025-02-19 at 12:30.