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Resolwe SDK for Python

Project description

Build Status Documentation Status Version on PyPI Supported Python versions Number of downloads from PyPI

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('me@mail.com', '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)

Project details


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Files for resdk, version 1.3.0
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