Python client

PyCellBase

• PyCellBase is a Python package that provides programmatic access to the comprehensive RESTful web service API that has been implemented for the CellBase database, providing an easy, lightweight, fast and intuitive access to it.
• It enables to query and obtain a wealth of biological information from a single database, saving a lot of time.
• As all information is integrated, queries about different biological topics can be easily and all this information can be linked together.
• More info about this package in the Python client tutorial of the CellBase Wiki

Package notes

• PyCellBase is compatible with both Python 2 and 3.
• This package makes use of multithreading to improve performance when the number of queries exceed a specific limit.
• It is distributed:
  • With the rest of the CellBase code at cellbase/clients/python.
  • Via PyPI - the Python Package Index

General usage

PyCellBase code can be accessed at https://github.com/opencb/cellbase/tree/develop/clients/python/pycellbase.

The CellBaseClient class provides access to the different clients of the data we want to query (e.g. gene, transcript, variation, protein, genomic region, variant).

Each of these clients provide a set of methods to ask for the resources we want to retrieve. Most of these methods will need to be provided with comma-separated IDs or list of IDs. Optional filters and extra options can be added as key-value parameters.

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

If there is an available resource, but there is not an available method in this python package, the CellBaseClient class can be used to create the URL of interest. This class is able to access the RESTful Web Services through the get method it implements. In this case, this method needs to be provided with those parameters which are required by the URL: category (e.g. feature), subcategory (e.g. gene), ID to search for (e.g. BRCA1) and method to query (e.g. search).

Configuration data as host, API version, or species is stored in a ConfigClient object. A custom configuration can be passed to CellBaseClient with a ConfigClient object provided with a JSON or YAML config file. If you want to change the configuration on the fly you can directly modify the ConfigClient object.

Please, find more details on how to use the python library at: Python client tutorial

Installation

Cloning

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

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

Once you have downloaded the project you can install the library:

$ cd cellbase/clients/python
$ python setup.py install

PyPI

PyCellBase is stored in PyPI and can be installed via pip:

$ pip install pycellbase