Python client pyCGA

pyCGA is the Python client library for OpenCGA RESTful Web Services, all the web services are accessible through this client, and it offers a quick way to query OpenCGA projects programmatically from custom scripts. For further information on how to install pyCGA please refer to RESTful Web Services and Clients#InstallingpyCGA. In the same way than in Using RESTful Web Services URL tutorial, we will focus on those end points more interesting for HGVA users. In order to make it easy to follow we will use the same examples used in Using RESTful Web Services URL.

First of all, configure and import the library:

Example of configuration file in JSON format

{
    "version": "v1",
    "rest": {
        "hosts": [
            "bioinfodev.hpc.cam.ac.uk/hgva-1.0"
        ]
    }
}

Example of configuration file in YAML format

---
version: v1
rest:
  hosts:
  - bioinfodev.hpc.cam.ac.uk/hgva-1.0

Example of configuration dictionary

configuration = {
    'version': 'v1',
    'rest': {
        'hosts': [
            'bioinfodev.hpc.cam.ac.uk/hgva-1.0'
        ]
    }
}

Load the configuration will be the first step, to use the python client. We will use the ConfigClient class, passing the name of the path of the configuration file or the dictionary with the configuration. After that the instance created will be passed to the Client.

Loading the configuration

from pyCGA.opencgaconfig import ConfigClient
from pyCGA.opencgarestclients import Studies, AnalysisVariant, Projects, Samples, Cohorts



# configuration = '/path/to/configuration_file.json'
# configuration = '/path/to/configuration_file.yaml'
configuration = {
    'version': 'v1',
    'rest': {
        'hosts': [
            '10.5.5.4:8080/opencga-test'
        ]
    }
}

# Initialise configuration
conf = ConfigClient(configuration)


# conf instance should be passed to the clients
study_client = Studies(conf)

Once the library is imported and configured, you can proceed to run the examples below.

Examples