============= 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

<pre> from biomart import BiomartServer </pre>

Connect to a Biomart Server

<pre> server = BiomartServer( "http://uswest.ensembl.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 </pre>

Interact with the biomart server

<pre> # 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 </pre>

Run a search

<pre> # 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' ] }) </pre>

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.

<pre> from biomart import BiomartDataset interpro = BiomartDataset( "http://www.biomart.org/biomart", name = 'entry' ) response = interpro.search({ 'filters': { 'entry_id': 'IPR027603' }, 'attributes': [ 'entry_name', 'abstract' ] }) </pre>