spirepy 0.2.0

A SPIRE wrapper and command-line tool for interacting with global microbiome data.

SPIREpy

• SPIREpy
  • Installation
  • Quickstart
  • Documentation
  • Credits

SPIREpy is a Python package and command-line tool that allows users to interact with the SPIRE database in a more convinient way.

Installation

SPIREpy is available on PyPI and can be installed via

pip install spirepy  

Quickstart

Python package

The Python package encapsulates the study and samples types from SPIRE into classes with properties that allow you to access and interact with their data. To load a study, we do:

from spirepy import Study

study = Study("Lloyd-Price_2019_HMP2IBD")

We can then obtain the list of samples that belong to this study.

study.get_samples()  

The study's metadata:

study.get_metadata()

Or even the assembled genomes:

study.get_mags()

Likewise, many of these attributes and operations are parallel to samples (Sample class) as well. For the full documentation and how to interact with them, see here

Command-line tool

The command-line interface tool allows the interaction with data from SPIRE directly in the terminal. It possesses 2 main interfaces:

• view
• download

These 2 sub-commands allows us to print tables and download data from both studies and samples. For more information on the available commands use:

spire --help

To view a study's metadata we can use:

spire --study view metadata Lloyd-Price_2019_HMP2IBD

And to download the same table as a .csv file we can instead:

spire --study download metadata Lloyd-Price_2019_HMP2IBD -o study/

Documentation

Documentation for the Python package and CLI tool can be found here.

Credits

These tools have been developed by the Big Data Biology Lab at the Centre for Microbiome Research at the Queensland University of Technology (Brisbane, Australia). It is part of the SPIRE: a Searchable, Planetary-scale mIcrobiome REsource project.

SPIRE is published in

Thomas S B Schmidt, Anthony Fullam, Pamela Ferretti, Askarbek Orakov, Oleksandr
M Maistrenko, Hans-Joachim Ruscheweyh, Ivica Letunic, Yiqian Duan, Thea Van
Rossum, Shinichi Sunagawa, Daniel R Mende, Robert D Finn, Michael Kuhn, Luis
Pedro Coelho, Peer Bork, SPIRE: a Searchable, Planetary-scale mIcrobiome
REsource, Nucleic Acids Research, Volume 52, Issue D1, 5 January 2024, Pages
D777–D783
https://doi.org/10.1093/nar/gkad943

Please cite this publication when referencing SPIREpy.