biomart 0.2.0

Python API that consumes the biomart webservice

Python API that consumes the biomart webservice.

What it will do:

• Show all databases of a biomart server

• Show all datasets of a biomart database

• Show attributes and filters of a biomart dataset

• Run your query formatted as a Python dict.

What it won’t do:

• Process and return the results as JSON,XML,etc. It will only return the Biomart response as TSV format.

Usage

Select a dataset

from biomart import BiomartDataset

interpro = BiomartDataset( "http://www.biomart.org/biomart", {'name': 'entry'} )

Use proxy

import os
interpro.http_proxy = os.environ.get('http_proxy', 'http://my_http_proxy.org')

Run query: Give me the name and abstract of interpro entry IPR027603

response = interpro.search({
  'filters': {
      'entry_id': 'IPR027603',
  },
  'attributes': [
      'entry_name', 'abstract'
  ]
})

# Returned format is TSV
for line in response.iter_lines():
  print line.split("\t")