pyCGA 1.3.0

A REST client for OpenCGA web services

Contents

• PyCGA

  • Installation

  • Usage

    • Getting started

    • What can I ask for?

PyCGA

• This Python package makes use of the exhaustive RESTful Web service API that has been implemented for the OpenCGA database.

• It provides easy access to OpenCGA, an open-source project that aims to provide a Big Data storage engine and analysis framework for genomic scale data analysis of hundreds of terabytes or even petabytes.

• More info about this project in the OpenCGA Wiki

Installation

Cloning

PyCGA 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:

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

Usage

Getting started

The first step is to set up the OpenCGA server configuration:

>>> configuration = {
        "version": "v1",
        "rest": {
            "hosts": ["http://100.15.26.35:8080/opencga"]
        }
    }

The configuration can be stored in a JSON or YML file as well:

>>> configuration = '/path/to/config/opencga_configuration.json'

The second step is to import the module and initialize the OpenCGAClient. Configuration, user and password must be specified:

>>> from pyCGA.opencgarestclients import OpenCGAClient
>>> oc = OpenCGAClient(configuration=configuration, user='user_example', pwd='pass_example')

If user and password are not desired to be written down in a script, session id can be used instead:

>>> from pyCGA.opencgarestclients import OpenCGAClient
>>> oc = OpenCGAClient(configuration=configuration, user='user_example', pwd='pass_example')  # Remove after getting session id
>>> print oc.session_id  # Remove after getting session id
"I4MG3fXJIZARl1LhwZ"
>>> oc = OpenCGAClient(configuration=configuration, session_id='I4MG3fXJIZARl1LhwZ')

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

>>> samples = oc.samples()  # Query for samples
>>> files = oc.files()  # Query for files
>>> cohorts = oc.cohorts()  # Query for cohorts

Now you can start asking to the OpenCGA RESTful service by providing a query ID:

>>> sample_search = samples.search(study='study1', name='sample1').get()
>>> print sample_search
"[{'acl': [{'member': '@gel', u'permissions': ['VIEW', 'VIEW_ANNOTATIONS']}..."

Responses are retrieved as JSON formatted data. Therefore, fields can be queried by key:

>>> creation_date = oc.samples.search(study='study1', name='sample1').get()[0]['creationDate']
"20170204822738"

First levels in the JSON output can be accessed as attributes:

>>> creation_date = samples.search(study='study1', name='sample1').get().creationDate
"20170204122738"

>>> annotation = cohorts.search(study='study1', name='cohort1').get().annotationSets
>>> print annotation[0]['annotations'][0]['value']['sex']
"F"

Regex are allowed in some fields. This is specially useful when searching by name:

>>> cohort_name = cohorts.search(study=study_id, name='~LP3000506-DNA_J01').get().name
>>> print cohort_name
"LP3000506-DNA_J01_LP3000924-DNA_Z02_0"

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

>>> creation_date = oc.samples.search(study='study1', name='sample1').get()[0]['creationDate']
"20170204822738"

>>> creation_date = oc.samples.search(study='study1', name='sample1').get()[1]['creationDate']
"20170204822738"

>>> creation_date = samples.search(study='study1', name='sample1,sample2').get().creationDate
["20170204122738", "20170204123049"]

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

>>> # e.g. "exclude" parameter
>>> attributes = oc.files.search(study='study1', name='~sample', bioformat='VARIANT', status='READY', exclude='attributes').get().attributes
>>> print attributes
[{}, {}, {}, {}, {}, {}, {}, {}]

>>> # e.g. "limit" parameter
>>> files = oc.files.search(study='study1', name='~sample', bioformat='VARIANT', status='READY', limit=1).get()
>>> print len(files)
1

Special mention for “analysis_variant” endpoint, which returns an iterator:

>>> variant_iterator = oc.analysis_variant.query(pag_size=100, data={'studies': 'study1', 'gene': 'BRCA2'}, limit=1)
>>> for variant in var_iterator:
>>>     print v.get().type
"SNV"

What can I ask for?

The best way to know which data can be retrieved for each client is either checking out the RESTful web services section of the OpenCGA Wiki or the OpenCGA web services