resdk

====================== Resolwe SDK for Python

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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.

.. _Resolwe Bioinformatics: https://github.com/genialis/resolwe-bio .. _Resolwe: https://github.com/genialis/resolwe

Docs & Help

Read the detailed description in documentation_.

.. _documentation: http://resdk.readthedocs.io/

Install

Install from PyPI::

pip install resdk

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

.. note::

If you are using Apple silicon you should use Python version 3.10 or higher.

.. _installation steps for developers: http://resdk.readthedocs.io/en/latest/contributing.html

Quick Start

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

.. code-block:: python

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_.

.. _Getting started: http://resdk.readthedocs.io/en/latest/tutorials.html

If you do not have access to the Resolwe server, contact us at [e-mail].