biomart

============= Biomart 0.9.2

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 and return the Biomart response as TSV format.

What it won't do:

• Process and return the results as JSON,XML,etc.

Usage

Import Biomart module ::

from biomart import BiomartServer

Connect to a Biomart Server ::

server = BiomartServer( "http://www.biomart.org/biomart" )

if you are behind a proxy

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

set verbose to True to get some messages

server.verbose = True

Interact with the biomart server ::

show server databases

server.show_databases() # uses pprint behind the scenes

show server datasets

server.show_datasets() # uses pprint behind the scenes

use the 'uniprot' dataset

uniprot = server.datasets['uniprot']

show all available filters and attributes of the 'uniprot' dataset

uniprot.show_filters() # uses pprint uniprot.show_attributes() # uses pprint

Run a search ::

run a search with the default attributes - equivalent to hitting "Results" on the web interface.

this will return a lot of data.

response = uniprot.search() response = uniprot.search( header = 1 ) # if you need the columns header

response format is TSV

for line in response.iter_lines(): line = line.decode('utf-8') print(line.split("\t"))

run a count - equivalent to hitting "Count" on the web interface

response = uniprot.count() print(response.text)

run a search with custom filters and default attributes.

response = uniprot.search({ 'filters': { 'accession': 'Q9FMA1' } }, header = 1 )

response = uniprot.search({ 'filters': { 'accession': ['Q9FMA1', 'Q8LFJ9'] # ID-list specified accessions } }, header = 1 )

run a search with custom filters and attributes (no header)

response = uniprot.search({ 'filters': { 'accession': ['Q9FMA1', 'Q8LFJ9'] }, 'attributes': [ 'accession', 'protein_name' ] })

Shortcut function: connect directly to a biomart dataset This is short in code but it might be long in time since the module needs to fetch all server's databases to find your dataset. ::

from biomart import BiomartDataset

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

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