SPIREpy is a Python package and command-line tool that allows users to interact with the SPIRE database in a more convinient way.
SPIREpy is available on PyPI and can be installed via
pip install spirepy
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
The command-line interface tool allows the interaction with data from SPIRE directly in the terminal. It possesses 2 main interfaces:
viewdownload
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 for the Python package and CLI tool can be found here.
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.