Metadata-Version: 1.1
Name: biomart
Version: 0.9.0
Summary: Python API that consumes the biomart webservice
Home-page: https://github.com/sebriois/biomart
Author: Sebastien Briois
Author-email: sebriois@gmail.com
License: BSD
Description: =============
        Biomart 0.9.0
        =============
        
        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' ]
          })
        
Keywords: bioinformatics biomart
Platform: UNKNOWN
Classifier: Environment :: Web Environment
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
