One Codex Python Client Library

Introduction

This package provides 3 major pieces of functionality: (1) a core Python client library; (2) a simple CLI for interacting with the One Codex platform that uses that core library; and (3) optional extensions to the client library, which offers many features aimed at advanced users and provides functionality for use in interactive notebook environments (e.g., Jupyter notebooks).

For installation instructions and instructions on using the command-line client, see the One Codex API - Python Client Library and CLI. You can find the source code on GitHub.

Installation

# The CLI (and core Python library)
pip install onecodex

# Optional dependencies (visualization, analysis and reports)
pip install onecodex[all]

Quickstart

import onecodex

# Instantiate the API (run onecodex login first)
ocx = onecodex.Api()

# Fetch some samples
project = ocx.Projects.get("d53ad03b010542e3")
samples = ocx.Samples.where(project=project, public=True, limit=10)

# Generate a Pandas DataFrame from classification results
results = samples.to_df()

# Plot a bar graph
# note: return_chart is not needed if using a Jupyter notebook
samples.plot_bargraph(return_chart=True)

Tutorials

For documentation and examples of common uses of the client library including interactive data analysis and plotting within Jupyter notebooks see Notebooks.

CLI

The Python package also comes with a command-line tool which can be used to upload samples to One Codex as well as results from the API. See One Codex API - Python Client Library and CLI for more information.