Python API that consumes the biomart webservice
Project description
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
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')
Interact with the biomart server
# show server databases print server.show_databases() # show server datasets print server.show_datasets() # use the 'uniprot' dataset uniprot = server.datasets['uniprot'] # run a search with the default filters and 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(): print line.split("\t") # run a count with the default filters and attributes - equivalent to hitting "Count" on the web interface response = uniprot.count() print response.text # show all available filters and attributes of the 'uniprot' dataset print uniprot.show_filters() print uniprot.show_attributes() # 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 response = uniprot.search({ 'filters': { 'accession': ['Q9FMA1', 'Q8LFJ9'] }, 'attributes': [ 'accession', 'protein_name' ] })
Shortcut function: connect directly to a biomart 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' ] })
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