resdk 1.3.0

Resolwe SDK for Python

The Resolwe SDK for Python supports writing tools for Resolwe dataflow package for Django framework and Resolwe Bioinformatics that includes the bioinformatics pipelines.

Docs & Help

Read detailed description in the documentation.

Install

To install, run:

pip install resdk

To install for development, run:

pip install -e .[docs,package,test]

Usage

Connect to the Resolwe server:

from resdk import Resolwe
re = Resolwe('[e-mail]', 'my_password', 'www.resolwe.com')

Get all collections and select the first one:

collections = re.collections()
collection = list(collections.values())[0]

Get expression objects and select the first one:

expressions = collection.data(type__startswith='data:expression:')
expression = expressions[0]

Print annotation:

expression.print_annotation()

Print file fields:

expression.print_downloads()

Download file:

filename = expression.annotation['output.exp']['value']['file']
file_stream = expression.download('output.exp')
with open(filename, 'w') as f:
    for part in file_stream:
        f.write(part)