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A simple pythonic interface to biomart.

Project description

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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

Documentation is available at: https://jrderuiter.github.io/pybiomart.

Examples

Retrieving and querying a dataset using the server interface:

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']})

License

Released under the MIT license.

Project details


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