{
    "info": {
        "author": "Chunlei Wu, Cyrus Afrasiabi, Sebastien Lelong",
        "author_email": "cwu@scripps.edu",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: OS Independent",
            "Operating System :: POSIX",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Utilities"
        ],
        "description": ".. image:: https://badge.fury.io/py/mygene.svg\n    :target: https://pypi.org/project/mygene/\n\n.. image:: https://img.shields.io/pypi/pyversions/mygene.svg\n    :target: https://pypi.org/project/mygene/\n\n.. image:: https://img.shields.io/pypi/format/mygene.svg\n    :target: https://pypi.org/project/mygene/\n\n.. image:: https://img.shields.io/pypi/status/mygene.svg\n    :target: https://pypi.org/project/mygene/\n\nIntro\n=====\n\nMyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data.\nIt's designed with simplicity and performance emphasized. ``mygene``, is an easy-to-use Python\nwrapper to access MyGene.Info_ services.\n\n.. _MyGene.Info: http://mygene.info\n.. _biothings_client: https://pypi.org/project/biothings-client/\n.. _mygene: https://pypi.org/project/mygene/\n\nAs of v3.1.0, mygene_ Python package is now a thin wrapper of underlying biothings_client_ package,\na universal Python client for all `BioThings APIs <http://biothings.io>`_, including MyGene.info_.\nThe installation of mygene_ will install biothings_client_ automatically. The following code snippets\nare essentially equivalent:\n\n\n* Continue using mygene_ package\n\n    .. code-block:: python\n\n        In [1]: import mygene\n        In [2]: mg = mygene.MyGeneInfo()\n\n* Use biothings_client_ package directly\n\n    .. code-block:: python\n\n        In [1]: from biothings_client import get_client\n        In [2]: mg = get_client('gene')\n\nAfter that, the use of ``mg`` instance is exactly the same, e.g. the usage examples below.\n\nRequirements\n============\n    python >=2.7 (including python3)\n\n    (Python 2.6 might still work, not it's not supported any more since v3.1.0.)\n\n    biothings_client_ (>=0.2.0, install using \"pip install biothings_client\")\n\nOptional dependencies\n======================\n    `pandas <http://pandas.pydata.org>`_ (install using \"pip install pandas\") is required for\n    returning a list of gene objects as `DataFrame <http://pandas.pydata.org/pandas-docs/stable/dsintro.html#dataframe>`_.\n\nInstallation\n=============\n\n    Option 1\n          pip install mygene\n\n    Option 2\n          download/extract the source code and run::\n\n           python setup.py install\n\n    Option 3\n          install the latest code directly from the repository::\n\n            pip install -e git+https://github.com/biothings/mygene.py#egg=mygene\n\nVersion history\n===============\n\n    `CHANGES.txt <https://raw.githubusercontent.com/SuLab/mygene.py/master/CHANGES.txt>`_\n\nTutorial\n=========\n\n* `ID mapping using mygene module in Python <http://nbviewer.ipython.org/6771106>`_\n\nDocumentation\n=============\n\n    http://mygene-py.readthedocs.org/\n\nUsage\n=====\n\n.. code-block:: python\n\n    In [1]: import mygene\n\n    In [2]: mg = mygene.MyGeneInfo()\n\n    In [3]: mg.getgene(1017)\n    Out[3]:\n    {'_id': '1017',\n     'entrezgene': 1017,\n     'name': 'cyclin-dependent kinase 2',\n     'symbol': 'CDK2',\n     'taxid': 9606}\n\n    In [4]: mg.getgene(1017, 'name,symbol,refseq')\n    Out[4]:\n    {'_id': '1017',\n     'name': 'cyclin-dependent kinase 2',\n     'refseq': {'genomic': ['AC_000144.1',\n       'NC_000012.11',\n       'NG_028086.1',\n       'NT_029419.12',\n       'NW_001838059.1'],\n      'protein': ['NP_001789.2', 'NP_439892.2'],\n      'rna': ['NM_001798.3', 'NM_052827.2']},\n     'symbol': 'CDK2'}\n\n    In [5]: mg.getgene(1017, 'name,symbol,refseq.rna')\n    Out[5]:\n    {'_id': '1017',\n     'name': 'cyclin-dependent kinase 2',\n     'refseq': {'rna': ['NM_001798', 'NM_052827']},\n     'symbol': 'CDK2'}\n\n\n    In [6]: mg.getgenes([1017,1018,'ENSG00000148795'])\n    Out[6]:\n    [{'_id': '1017',\n      'entrezgene': 1017,\n      'name': 'cyclin-dependent kinase 2',\n      'query': '1017',\n      'symbol': 'CDK2',\n      'taxid': 9606},\n     {'_id': '1018',\n      'entrezgene': 1018,\n      'name': 'cyclin-dependent kinase 3',\n      'query': '1018',\n      'symbol': 'CDK3',\n      'taxid': 9606},\n     {'_id': '1586',\n      'entrezgene': 1586,\n      'name': 'cytochrome P450, family 17, subfamily A, polypeptide 1',\n      'query': 'ENSG00000148795',\n      'symbol': 'CYP17A1',\n      'taxid': 9606}]\n\n    In [7]: mg.getgenes([1017,1018,'ENSG00000148795'], as_dataframe=True)\n    Out[7]:\n                      _id  entrezgene  \\\n    query\n    1017             1017        1017\n    1018             1018        1018\n    ENSG00000148795  1586        1586\n\n                                                                  name   symbol  \\\n    query\n    1017                                     cyclin-dependent kinase 2     CDK2\n    1018                                     cyclin-dependent kinase 3     CDK3\n    ENSG00000148795  cytochrome P450, family 17, subfamily A, polyp...  CYP17A1\n\n                     taxid\n    query\n    1017              9606\n    1018              9606\n    ENSG00000148795   9606\n\n    [3 rows x 5 columns]\n\n    In [8]:  mg.query('cdk2', size=5)\n    Out[8]:\n    {'hits': [{'_id': '1017',\n       '_score': 373.24667,\n       'entrezgene': 1017,\n       'name': 'cyclin-dependent kinase 2',\n       'symbol': 'CDK2',\n       'taxid': 9606},\n      {'_id': '12566',\n       '_score': 353.90176,\n       'entrezgene': 12566,\n       'name': 'cyclin-dependent kinase 2',\n       'symbol': 'Cdk2',\n       'taxid': 10090},\n      {'_id': '362817',\n       '_score': 264.88477,\n       'entrezgene': 362817,\n       'name': 'cyclin dependent kinase 2',\n       'symbol': 'Cdk2',\n       'taxid': 10116},\n      {'_id': '52004',\n       '_score': 21.221401,\n       'entrezgene': 52004,\n       'name': 'CDK2-associated protein 2',\n       'symbol': 'Cdk2ap2',\n       'taxid': 10090},\n      {'_id': '143384',\n       '_score': 18.617256,\n       'entrezgene': 143384,\n       'name': 'CDK2-associated, cullin domain 1',\n       'symbol': 'CACUL1',\n       'taxid': 9606}],\n     'max_score': 373.24667,\n     'took': 10,\n     'total': 28}\n\n    In [9]: mg.query('reporter:1000_at')\n    Out[9]:\n    {'hits': [{'_id': '5595',\n       '_score': 11.163337,\n       'entrezgene': 5595,\n       'name': 'mitogen-activated protein kinase 3',\n       'symbol': 'MAPK3',\n       'taxid': 9606}],\n     'max_score': 11.163337,\n     'took': 6,\n     'total': 1}\n\n    In [10]: mg.query('symbol:cdk2', species='human')\n    Out[10]:\n    {'hits': [{'_id': '1017',\n       '_score': 84.17707,\n       'entrezgene': 1017,\n       'name': 'cyclin-dependent kinase 2',\n       'symbol': 'CDK2',\n       'taxid': 9606}],\n     'max_score': 84.17707,\n     'took': 27,\n     'total': 1}\n\n    In [11]: mg.querymany([1017, '695'], scopes='entrezgene', species='human')\n    Finished.\n    Out[11]:\n    [{'_id': '1017',\n      'entrezgene': 1017,\n      'name': 'cyclin-dependent kinase 2',\n      'query': '1017',\n      'symbol': 'CDK2',\n      'taxid': 9606},\n     {'_id': '695',\n      'entrezgene': 695,\n      'name': 'Bruton agammaglobulinemia tyrosine kinase',\n      'query': '695',\n      'symbol': 'BTK',\n      'taxid': 9606}]\n\n    In [12]: mg.querymany([1017, '695'], scopes='entrezgene', species=9606)\n    Finished.\n    Out[12]:\n    [{'_id': '1017',\n      'entrezgene': 1017,\n      'name': 'cyclin-dependent kinase 2',\n      'query': '1017',\n      'symbol': 'CDK2',\n      'taxid': 9606},\n     {'_id': '695',\n      'entrezgene': 695,\n      'name': 'Bruton agammaglobulinemia tyrosine kinase',\n      'query': '695',\n      'symbol': 'BTK',\n      'taxid': 9606}]\n\n    In [13]: mg.querymany([1017, '695'], scopes='entrezgene', species=9606, as_dataframe=True)\n    Finished.\n    Out[13]:\n            _id  entrezgene                                       name symbol  \\\n    query\n    1017   1017        1017                  cyclin-dependent kinase 2   CDK2\n    695     695         695  Bruton agammaglobulinemia tyrosine kinase    BTK\n\n           taxid\n    query\n    1017    9606\n    695     9606\n\n    [2 rows x 5 columns]\n\n    In [14]: mg.querymany([1017, '695', 'NA_TEST'], scopes='entrezgene', species='human')\n    Finished.\n    Out[14]:\n    [{'_id': '1017',\n      'entrezgene': 1017,\n      'name': 'cyclin-dependent kinase 2',\n      'query': '1017',\n      'symbol': 'CDK2',\n      'taxid': 9606},\n     {'_id': '695',\n      'entrezgene': 695,\n      'name': 'Bruton agammaglobulinemia tyrosine kinase',\n      'query': '695',\n      'symbol': 'BTK',\n      'taxid': 9606},\n     {'notfound': True, 'query': 'NA_TEST'}]\n\n    # query all human kinases using fetch_all parameter:\n    In [15]: kinases = mg.query('name:kinase', species='human', fetch_all=True)\n    In [16]: kinases\n    Out [16]\" <generator object _fetch_all at 0x7fec027d2eb0>\n\n    # kinases is a Python generator, now you can loop through it to get all 1073 hits:\n    In [16]: for gene in kinases:\n       ....:     print gene['_id'], gene['symbol']\n    Out [16]: <output omitted here>\n\n\nContact\n========\nDrop us any question or feedback:\n    * biothings@googlegroups.com  (public discussion)\n    * help@mygene.info (reach devs privately)\n    * `Github issues <https://github.com/biothings/mygene.info/issues>`_\n    * on twitter `@mygeneinfo <https://twitter.com/mygeneinfo>`_\n    * Post a question on `BioStars.org <https://www.biostars.org/p/new/post/?tag_val=mygene>`_ with tag #mygene.\n\n\n\n",
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