{ "info": { "author": "Sebastien Briois", "author_email": "sebriois@gmail.com", "bugtrack_url": null, "classifiers": [ "Environment :: Web Environment", "Intended Audience :: Developers", "License :: OSI Approved :: BSD License", "Operating System :: OS Independent", "Programming Language :: Python", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "=============\nBiomart 0.9.2\n=============\n\nPython API that consumes the biomart webservice.\n\nWhat it will do:\n----------------\n\n* Show all databases of a biomart server\n* Show all datasets of a biomart database\n* Show attributes and filters of a biomart dataset\n* Run your query formatted as a Python dict and return the Biomart response as TSV format.\n\nWhat it won't do:\n-----------------\n\n* Process and return the results as JSON,XML,etc.\n\nUsage\n-----\n\nImport Biomart module\n::\n \n from biomart import BiomartServer\n\nConnect to a Biomart Server\n::\n \n server = BiomartServer( \"http://www.biomart.org/biomart\" )\n \n # if you are behind a proxy\n import os\n server.http_proxy = os.environ.get('http_proxy', 'http://my_http_proxy.org')\n\n # set verbose to True to get some messages\n server.verbose = True\n\nInteract with the biomart server\n::\n \n # show server databases\n server.show_databases() # uses pprint behind the scenes\n \n # show server datasets\n server.show_datasets() # uses pprint behind the scenes\n \n # use the 'uniprot' dataset\n uniprot = server.datasets['uniprot']\n\n # show all available filters and attributes of the 'uniprot' dataset\n uniprot.show_filters() # uses pprint\n uniprot.show_attributes() # uses pprint\n\n\nRun a search\n::\n\n # run a search with the default attributes - equivalent to hitting \"Results\" on the web interface.\n # this will return a lot of data.\n response = uniprot.search()\n response = uniprot.search( header = 1 ) # if you need the columns header\n \n # response format is TSV\n for line in 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