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 (spirepy.sample.Sample) as well.

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/