pyopencga 1.4.0

A REST client for OpenCGA REST web services

Contents

• PyOpenCGA

  • Installation

    • Cloning

    • Pip install

  • Usage

    • Import pyOpenCGA package

    • Setting up server host configuration

    • Log in to OpenCGA host server

    • Examples

    • What can I ask for?

PyOpenCGA

This Python client package makes use of the comprehensive RESTful web services API implemented for the OpenCGA platform. OpenCGA is an open-source project that implements a high-performance, scalable and secure platform for Genomic data analysis and visualisation

OpenCGA implements a secure and high performance platform for Big Data analysis and visualisation in current genomics. OpenCGA uses the most modern and advanced technologies to scale to petabytes of data. OpenCGA is designed and implemented to work with few million genomes. It is built on top of three main components: Catalog, Variant and Alignment Storage and Analysis.

More info about this project in the OpenCGA Docs

Installation

Cloning

PyOpenCGA can be cloned in your local machine by executing in your terminal:

$ git clone https://github.com/opencb/opencga.git

Once you have downloaded the project you can install the library. We recommend to install it inside a virtual environment:

$ cd opencga/tree/develop/opencga-client/src/main/python/pyOpenCGA
$ python setup.py install

Pip install

Run the following command in the shell:

$ pip install pyopencga

Usage

Import pyOpenCGA package

The first step is to import the ConfigClient and OpenCGAClient from pyOpenCGA:

>>> from pyopencga.opencga_config import ConfigClient
>>> from pyopencga.opencga_client import OpenCGAClient

Setting up server host configuration

The second step is to set up the OpenCGA host server configuration you can get a basic configuration dictionary specifying your OpenCGA server host:

>>> host = 'http://bioinfodev.hpc.cam.ac.uk/opencga-test' # Use a server host where you have an account
>>> cc = ConfigClient()
>>> config_dict = cc.get_basic_config_dict(host)
>>> print(config_dict)
{'version': 'v1', 'rest': {'hosts': ['http://bioinfodev.hpc.cam.ac.uk/opencga-test']}}

Log in to OpenCGA host server

With this configuration you can initialize the OpenCGAClient and log into an OpenCGA user account, specifying a user and password:

>>> oc = OpenCGAClient(configuration=config_dict,user='user_id',pwd='user_password')

For scripting or using Jupyter Notebooks is preferable to load user credentials from an external JSON file.

Once you are logged in, it is mandatory to use the token of the session to propagate the access of the clients to the host server:

>>> token = oc.session_id
>>> print(token)
eyJhbGciOi...

>>> oc = OpenCGAClient(configuration=config_dict, session_id=token)

Examples

The next step is to create the specific client for the data we want to query:

>>> projects = oc.projects # Query for projects
>>> studies = oc.studies # Query for studies
>>> samples = oc.samples()  # Query for samples
>>> cohorts = oc.cohorts()  # Query for cohorts

Now you can start asking to the OpenCGA RESTful service with pyOpenCGA:

>>> for project in projects.search(owner=user).results():
...    print(project['id'])
project1
project2
[...]

There are four different ways to access to the query response data:

>>> foo_client.method().first() # Returns the first QueryResult
>>> foo_client.method().result(position=0) # Returns the result from all QueryResults in a given position
>>> foo_client.method().results() # Iterates over all the results of all the QueryResults
>>> foo_client.method().response # Returns the raw response of the QueryResponse

Data can be accessed specifying comma-separated IDs or a list of IDs:

>>> samples = 'NA12877,NA12878,NA12879'
>>> samples_list = ['NA12877','NA12878','NA12879']
>>> sc = oc.samples

>>> for result in sc.info(query_id=samples, study='user@project1:study1').results():
...     print(result['id'], result['attributes']['OPENCGA_INDIVIDUAL']['disorders'])
NA12877 [{'id': 'OMIM6500', 'name': "Chron's Disease"}]
NA12878 []
NA12879 [{'id': 'OMIM6500', 'name': "Chron's Disease"}]

>>> for result in sc.info(query_id=samples_list, study='user@project1:study1').results():
...     print(result['id'], result['attributes']['OPENCGA_INDIVIDUAL']['disorders'])
NA12877 [{'id': 'OMIM6500', 'name': "Chron's Disease"}]
NA12878 []
NA12879 [{'id': 'OMIM6500', 'name': "Chron's Disease"}]

Optional filters and extra options can be added as key-value parameters (where the values can be a comma-separated string or a list).

What can I ask for?

The best way to know which data can be retrieved for each client check OpenCGA web services swagger.