pybiomart 0.1

A simple pythonic interface to biomart.

A simple and pythonic biomart interface for Python.

The intent of pybiomart is to provide a simple interface to biomart, which can be used to easily query biomart databases from Python. In this sense, pybiomart aims to provide functionality similar to packages such as biomaRt (which provides access to biomart from R).

Documentation

Detailed documentation is available at: https://pybiomart.readthedocs.org.

Examples

Retrieving and querying a dataset using the server interace:

from pybiomart import Server

server = Server(host='http://www.ensembl.org')

dataset = (server.marts['ENSEMBL_MART_ENSEMBL']
                 .datasets['hsapiens_gene_ensembl'])

dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'],
              filters={'chromosome_name': ['1','2']})

Retrieving a dataset directly with known dataset name:

from pybiomart import Dataset

dataset = Dataset(name='hsapiens_gene_ensembl',
                  host='http://www.ensembl.org')

dataset.query(attributes=['ensembl_gene_id', 'external_gene_name'],
              filters={'chromosome_name': ['1','2']})

Installation

The source code is currently hosted on GitHub at: https://github.com/jrderuiter/pybiomart.

The package can be installed from pypi via pip:

pip install pybiomart

The development version can be installed from GitHub:

pip install git+https://github.com/jrderuiter/pybiomart.git#egg=pybiomart

Dependencies

• Python 3.3+, Python 2.7

• future, pandas, requests, requests-cache

License

Released under the MIT license.