Resolwe SDK for Python

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

Install

Install from PyPI:

pip install resdk

Warning

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 platform 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 code base, follow the installation steps for developers.

Usage example

We will download a sample containing raw sequencing reads that were aligned to a genome:

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()

Multiple files (fastq, fastQC report, bam, bai…) have downloaded to the working directory. Check them out. To learn more about the Resolwe SDK continue with Tutorials.

If you have problems connecting to our server, please contact us at info@genialis.com.