spirepy 0.1.0

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

SPIREpy

• SPIREpy
  • Usage
  • Documentation
  • Installation
  • Credits

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

Usage

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/

Installation

TODO: need to add to PyPI and conda first

Documentation

TODO: need readthedocs

Credits