Metadata-Version: 1.1
Name: mygene
Version: 1.0.0
Summary: Python Client for MyGene.Info services.
Home-page: https://bitbucket.org/newgene/mygene
Author: Chunlei Wu
Author-email: cwu@scripps.edu
License: BSD
Description: Intro
        =====
        
        MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It's designed with simplicity and performance emphasized. *mygene*, is an easy-to-use Python wrapper to access MyGene.Info_ services.
        
        .. _MyGene.Info: http://mygene.info
        .. _httplib2: http://code.google.com/p/httplib2/
        
        Requirements
        ============
            httplib2_ (install using "pip install httplib2")
        
        
        Installation
        =============
        
            Option 1
                  pip install mygene
        
            Options 2
                  download/extract the source code and run::
                   python setup install
        
            Option 3
                  install the latest code directly from the repository::
                    pip install -e hg+https://bitbucket.org/newgene/mygene#egg=mygene
        
        
        Usage
        =====
        
        ::
        
            In [1]: import mygene
        
            In [2]: mg = mygene.MyGeneInfo()
        
            In [3]: mg.getgene(1017)
            Out[3]: {'_id': '1017', 'name': 'cyclin-dependent kinase 2', 'symbol': 'CDK2'}
        
            In [4]: mg.getgene(1017, 'name,symbol,refseq')
            Out[4]:
            {'_id': '1017',
             'name': 'cyclin-dependent kinase 2',
             'refseq': {'genomic': ['AC_000144.1',
               'NC_000012.11',
               'NG_028086.1',
               'NT_029419.12',
               'NW_001838059.1'],
              'protein': ['NP_001789.2', 'NP_439892.2'],
              'rna': ['NM_001798.3', 'NM_052827.2']},
             'symbol': 'CDK2'}
        
            In [5]: mg.getgene(1017, 'name,symbol,refseq.rna')
            Out[5]:
            {'_id': '1017',
             'name': 'cyclin-dependent kinase 2',
             'refseq': {'rna': ['NM_001798.3', 'NM_052827.2']},
             'symbol': 'CDK2'}
        
        
            In [6]: mg.getgenes([1017,1018,'ENSG00000148795'])
            Out[6]:
            [{'_id': '1017', 'name': 'cyclin-dependent kinase 2', 'symbol': 'CDK2'},
             {'_id': '1018', 'name': 'cyclin-dependent kinase 3', 'symbol': 'CDK3'},
             {'_id': '1586',
              'name': 'cytochrome P450, family 17, subfamily A, polypeptide 1',
              'symbol': 'CYP17A1'}]
        
        
            In [7]:  mg.query('cdk2', limit=5)
            Out[7]:
            {'etag': '1358e787924ddb',
             'limit': 5,
             'rows': [{'id': '684247',
               'name': 'similar to S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1)',
               'score': 2.615727663040161,
               'symbol': 'LOC684247',
               'taxid': 10116},
              {'id': '681208',
               'name': 'similar to S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1)',
               'score': 2.288761615753174,
               'symbol': 'LOC681208',
               'taxid': 10116},
              {'id': '690181',
               'name': 'similar to S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1)',
               'score': 2.288761615753174,
               'symbol': 'LOC690181',
               'taxid': 10116},
              {'id': '690646',
               'name': 'similar to S-phase kinase-associated protein 2 (F-box protein Skp2) (Cyclin A/CDK2-associated protein p45) (F-box/WD-40 protein 1) (FWD1)',
               'score': 1.9617958068847656,
               'symbol': 'LOC690646',
               'taxid': 10116},
              {'id': '687002',
               'name': 'similar to S-phase kinase-associated protein 2 (F-box protein Skp2) (Cyclin A/CDK2-associated protein p45) (F-box/WD-40 protein 1) (FWD1)',
               'score': 1.9617958068847656,
               'symbol': 'LOC687002',
               'taxid': 10116}],
             'skip': 0,
             'total_rows': 29}
        
            In [8]: mg.query('reporter:1000_at')
            Out[8]:
            {'etag': '13574eee908e81',
             'limit': 25,
             'rows': [{'homologene': {'genes': [[9606, 5595],
                 [10090, 26417],
                 [10116, 50689],
                 [7955, 399480],
                 [3702, 837559],
                 [3702, 842248]],
                'id': 55682},
               'id': '5595',
               'name': 'mitogen-activated protein kinase 3',
               'score': 8.231849670410156,
               'symbol': 'MAPK3',
               'taxid': 9606}],
             'skip': 0,
             'total_rows': 1}
        
            In [9]: mg.query('symbol:cdk2 AND species:human')
            Out[9]:
            {'etag': '1358e787924ddb',
             'limit': 25,
             'rows': [{'homologene': {'genes': [[9606, 1017],
                 [10090, 12566],
                 [10116, 362817],
                 [7227, 42453],
                 [7955, 406715],
                 [3702, 824036]],
                'id': 74409},
               'id': '1017',
               'name': 'cyclin-dependent kinase 2',
               'score': 71.34159851074219,
               'symbol': 'CDK2',
               'taxid': 9606}],
             'skip': 0,
             'total_rows': 1}
        
        
        
            In [10]: mg.findgenes([1017, '695'], scope='entrezgene', species='human')
            querying 1-2...
            Finished.
            Out[10]:
            [(1017, '1017', 'CDK2', 'cyclin-dependent kinase 2'),
             ('695', '695', 'BTK', 'Bruton agammaglobulinemia tyrosine kinase')]
        
            In [11]: mg.findgenes([1017, '695'], scope='entrezgene', species=9606)
            querying 1-2...
            Finished.
            Out[11]:
            [(1017, '1017', 'CDK2', 'cyclin-dependent kinase 2'),
             ('695', '695', 'BTK', 'Bruton agammaglobulinemia tyrosine kinase')]
        
            In [12]: mg.findgenes([1017, '695', 'NA_TEST'], scope='entrezgene', species='human')
            querying 1-3...
            Finished.
            1 input ids found no hit:
                 ['NA_TEST']
            Out[12]:
            [(1017, '1017', 'CDK2', 'cyclin-dependent kinase 2'),
             ('695', '695', 'BTK', 'Bruton agammaglobulinemia tyrosine kinase'),
             ('NA_TEST', '', '', '')]
        
            In [13]: mg.findgenes([1017, '695', 'NA_TEST'], scope='entrezgene', species='human', raw=True)
            querying 1-3...
            Finished.
            Out[13]:
            [{'homologene': {'genes': [[9606, 1017],
                                       [10090, 12566],
                                       [10116, 362817],
                                       [7227, 42453],
                                       [7955, 406715],
                                       [3702, 824036]],
                              'id': 74409},
              'id': '1017',
              'key': ['1017', 'entrezgene'],
              'name': 'cyclin-dependent kinase 2',
              'symbol': 'CDK2',
              'taxid': 9606},
             {'homologene': {'genes': [[9606, 695],
                                       [10090, 12229],
                                       [10116, 367901],
                                       [7955, 568653]],
                             'id': 30953},
              'id': '695',
              'key': ['695', 'entrezgene'],
              'name': 'Bruton agammaglobulinemia tyrosine kinase',
              'symbol': 'BTK',
              'taxid': 9606}]
        
        
        
        Contact
        ========
        Drop us any feedback at: help@mygene.info
        
Keywords: biology gene annotation web service client api
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Utilities
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
