gregorjerse / resolwe-bio-py

Resolwe Bioinformatics Python API

Resolwe SDK for Python

Resolwe SDK for Python supports interaction with Resolwe server and its extension Resolwe Bioinformatics. You can use it to upload and inspect biomedical data sets, contribute annotations, run analysis, and write pipelines.

Docs & Help

Read the detailed description in documentation.

Install

Install from PyPI:

pip install resdk

If you use macOS, be aware that the version of Python shipped with the system doesn't support TLSv1.2, which is required for connecting to any genialis.com server (and probably others). To solve the issue, install the latest version of Python 3.6+ via official installer from Python.org or with Homebrew.

If you would like to contribute to the SDK codebase, follow the installation steps for developers.

Quick Start

In this showcase we will download the aligned reads and their index (BAM and BAI) from the server:

import resdk

# Create a Resolwe object to interact with the server
res = resdk.Resolwe(url='https://app.genialis.com')

# Enable verbose logging to standard output
resdk.start_logging()

# Get sample meta-data from the server
sample = res.sample.get('resdk-example')

# Download files associated with the sample
sample.download()

Both files (BAM and BAI) have downloaded to the working directory. Check them out. To learn more about the Resolwe SDK continue with Getting started.

If you do not have access to the Resolwe server, contact us at [email protected].