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+Metadata-Version: 2.1
+Name: mygene
+Version: 3.2.2
+Summary: Python Client for MyGene.Info services.
+Home-page: https://github.com/biothings/mygene.py
+Author: Chunlei Wu, Cyrus Afrasiabi, Sebastien Lelong
+Author-email: cwu@scripps.edu
+License: BSD
+Keywords: biology gene annotation web service client api
+Platform: UNKNOWN
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 2
+Classifier: Programming Language :: Python :: 2.7
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.4
+Classifier: Programming Language :: Python :: 3.5
+Classifier: Programming Language :: Python :: 3.6
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: Topic :: Utilities
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Dist: biothings-client (>=0.2.6)
+
+.. image:: https://pepy.tech/badge/mygene
+    :target: https://pepy.tech/project/mygene
+
+.. image:: https://img.shields.io/pypi/dm/mygene.svg
+    :target: https://pypistats.org/packages/mygene
+
+.. image:: https://badge.fury.io/py/mygene.svg
+    :target: https://pypi.org/project/mygene/
+
+.. image:: https://img.shields.io/pypi/pyversions/mygene.svg
+    :target: https://pypi.org/project/mygene/
+
+.. image:: https://img.shields.io/pypi/format/mygene.svg
+    :target: https://pypi.org/project/mygene/
+
+.. image:: https://img.shields.io/pypi/status/mygene.svg
+    :target: https://pypi.org/project/mygene/
+
+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
+.. _biothings_client: https://pypi.org/project/biothings-client/
+.. _mygene: https://pypi.org/project/mygene/
+
+Since v3.1.0, mygene_ Python package has become a thin wrapper of underlying biothings_client_ package,
+a universal Python client for all `BioThings APIs <http://biothings.io>`_, including MyGene.info_.
+The installation of mygene_ will install biothings_client_ automatically. The following code snippets
+are essentially equivalent:
+
+
+* Continue using mygene_ package
+
+    .. code-block:: python
+
+        In [1]: import mygene
+        In [2]: mg = mygene.MyGeneInfo()
+
+* Use biothings_client_ package directly
+
+    .. code-block:: python
+
+        In [1]: from biothings_client import get_client
+        In [2]: mg = get_client('gene')
+
+After that, the use of ``mg`` instance is exactly the same, e.g. the usage examples below.
+
+Requirements
+============
+    python >=2.7 (including python3)
+
+    (Python 2.6 might still work, but it's not supported any more since v3.1.0.)
+
+    biothings_client_ (>=0.2.0, install using "pip install biothings_client")
+
+Optional dependencies
+======================
+    `pandas <http://pandas.pydata.org>`_ (install using "pip install pandas") is required for
+    returning a list of gene objects as `DataFrame <http://pandas.pydata.org/pandas-docs/stable/dsintro.html#dataframe>`_.
+
+Installation
+=============
+
+    Option 1
+          pip install mygene
+
+    Option 2
+          download/extract the source code and run::
+
+           python setup.py install
+
+    Option 3
+          install the latest code directly from the repository::
+
+            pip install -e git+https://github.com/biothings/mygene.py#egg=mygene
+
+Version history
+===============
+
+    `CHANGES.txt <https://raw.githubusercontent.com/SuLab/mygene.py/master/CHANGES.txt>`_
+
+Tutorial
+=========
+
+* `ID mapping using mygene module in Python <http://nbviewer.ipython.org/6771106>`_
+
+Documentation
+=============
+
+    http://mygene-py.readthedocs.org/
+
+Usage
+=====
+
+.. code-block:: python
+
+    In [1]: import mygene
+
+    In [2]: mg = mygene.MyGeneInfo()
+
+    In [3]: mg.getgene(1017)
+    Out[3]:
+    {'_id': '1017',
+     'entrezgene': 1017,
+     'name': 'cyclin-dependent kinase 2',
+     'symbol': 'CDK2',
+     'taxid': 9606,
+     ...
+    }
+
+    # use "fields" parameter to return a subset of fields
+    In [4]: mg.getgene(1017, fields='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, fields=['name', 'symbol', 'refseq.rna'])
+    Out[5]:
+    {'_id': '1017',
+     'name': 'cyclin-dependent kinase 2',
+     'refseq': {'rna': ['NM_001798.5', 'NM_052827.3']},
+     'symbol': 'CDK2'}
+
+
+    In [6]: mg.getgenes([1017,1018,'ENSG00000148795'], fields='name,symbol,entrezgene,taxid')
+    Out[6]:
+    [{'_id': '1017',
+      'entrezgene': 1017,
+      'name': 'cyclin-dependent kinase 2',
+      'query': '1017',
+      'symbol': 'CDK2',
+      'taxid': 9606},
+     {'_id': '1018',
+      'entrezgene': 1018,
+      'name': 'cyclin-dependent kinase 3',
+      'query': '1018',
+      'symbol': 'CDK3',
+      'taxid': 9606},
+     {'_id': '1586',
+      'entrezgene': 1586,
+      'name': 'cytochrome P450, family 17, subfamily A, polypeptide 1',
+      'query': 'ENSG00000148795',
+      'symbol': 'CYP17A1',
+      'taxid': 9606}]
+
+    # return results in Pandas DataFrame
+    In [7]: mg.getgenes([1017,1018,'ENSG00000148795'], fields='name,symbol,entrezgene,taxid', as_dataframe=True)
+    Out[7]:
+                      _id  entrezgene  \
+    query
+    1017             1017        1017
+    1018             1018        1018
+    ENSG00000148795  1586        1586
+
+                                                                  name   symbol  \
+    query
+    1017                                     cyclin-dependent kinase 2     CDK2
+    1018                                     cyclin-dependent kinase 3     CDK3
+    ENSG00000148795  cytochrome P450, family 17, subfamily A, polyp...  CYP17A1
+
+                     taxid
+    query
+    1017              9606
+    1018              9606
+    ENSG00000148795   9606
+
+    [3 rows x 5 columns]
+
+    In [8]:  mg.query('cdk2', size=5)
+    Out[8]:
+    {'hits': [{'_id': '1017',
+       '_score': 373.24667,
+       'entrezgene': 1017,
+       'name': 'cyclin-dependent kinase 2',
+       'symbol': 'CDK2',
+       'taxid': 9606},
+      {'_id': '12566',
+       '_score': 353.90176,
+       'entrezgene': 12566,
+       'name': 'cyclin-dependent kinase 2',
+       'symbol': 'Cdk2',
+       'taxid': 10090},
+      {'_id': '362817',
+       '_score': 264.88477,
+       'entrezgene': 362817,
+       'name': 'cyclin dependent kinase 2',
+       'symbol': 'Cdk2',
+       'taxid': 10116},
+      {'_id': '52004',
+       '_score': 21.221401,
+       'entrezgene': 52004,
+       'name': 'CDK2-associated protein 2',
+       'symbol': 'Cdk2ap2',
+       'taxid': 10090},
+      {'_id': '143384',
+       '_score': 18.617256,
+       'entrezgene': 143384,
+       'name': 'CDK2-associated, cullin domain 1',
+       'symbol': 'CACUL1',
+       'taxid': 9606}],
+     'max_score': 373.24667,
+     'took': 10,
+     'total': 28}
+
+    In [9]: mg.query('reporter:1000_at')
+    Out[9]:
+    {'hits': [{'_id': '5595',
+       '_score': 11.163337,
+       'entrezgene': 5595,
+       'name': 'mitogen-activated protein kinase 3',
+       'symbol': 'MAPK3',
+       'taxid': 9606}],
+     'max_score': 11.163337,
+     'took': 6,
+     'total': 1}
+
+    In [10]: mg.query('symbol:cdk2', species='human')
+    Out[10]:
+    {'hits': [{'_id': '1017',
+       '_score': 84.17707,
+       'entrezgene': 1017,
+       'name': 'cyclin-dependent kinase 2',
+       'symbol': 'CDK2',
+       'taxid': 9606}],
+     'max_score': 84.17707,
+     'took': 27,
+     'total': 1}
+
+    In [11]: mg.querymany([1017, '695'], scopes='entrezgene', species='human')
+    Finished.
+    Out[11]:
+    [{'_id': '1017',
+      'entrezgene': 1017,
+      'name': 'cyclin-dependent kinase 2',
+      'query': '1017',
+      'symbol': 'CDK2',
+      'taxid': 9606},
+     {'_id': '695',
+      'entrezgene': 695,
+      'name': 'Bruton agammaglobulinemia tyrosine kinase',
+      'query': '695',
+      'symbol': 'BTK',
+      'taxid': 9606}]
+
+    In [12]: mg.querymany([1017, '695'], scopes='entrezgene', species=9606)
+    Finished.
+    Out[12]:
+    [{'_id': '1017',
+      'entrezgene': 1017,
+      'name': 'cyclin-dependent kinase 2',
+      'query': '1017',
+      'symbol': 'CDK2',
+      'taxid': 9606},
+     {'_id': '695',
+      'entrezgene': 695,
+      'name': 'Bruton agammaglobulinemia tyrosine kinase',
+      'query': '695',
+      'symbol': 'BTK',
+      'taxid': 9606}]
+
+    In [13]: mg.querymany([1017, '695'], scopes='entrezgene', species=9606, as_dataframe=True)
+    Finished.
+    Out[13]:
+            _id  entrezgene                                       name symbol  \
+    query
+    1017   1017        1017                  cyclin-dependent kinase 2   CDK2
+    695     695         695  Bruton agammaglobulinemia tyrosine kinase    BTK
+
+           taxid
+    query
+    1017    9606
+    695     9606
+
+    [2 rows x 5 columns]
+
+    In [14]: mg.querymany([1017, '695', 'NA_TEST'], scopes='entrezgene', species='human')
+    Finished.
+    Out[14]:
+    [{'_id': '1017',
+      'entrezgene': 1017,
+      'name': 'cyclin-dependent kinase 2',
+      'query': '1017',
+      'symbol': 'CDK2',
+      'taxid': 9606},
+     {'_id': '695',
+      'entrezgene': 695,
+      'name': 'Bruton agammaglobulinemia tyrosine kinase',
+      'query': '695',
+      'symbol': 'BTK',
+      'taxid': 9606},
+     {'notfound': True, 'query': 'NA_TEST'}]
+
+    # query all human kinases using fetch_all parameter:
+    In [15]: kinases = mg.query('name:kinase', species='human', fetch_all=True)
+    In [16]: kinases
+    Out [16]" <generator object _fetch_all at 0x7fec027d2eb0>
+
+    # kinases is a Python generator, now you can loop through it to get all 1073 hits:
+    In [16]: for gene in kinases:
+       ....:     print gene['_id'], gene['symbol']
+    Out [16]: <output omitted here>
+
+
+Contact
+========
+Drop us any question or feedback:
+    * biothings@googlegroups.com  (public discussion)
+    * help@mygene.info (reach devs privately)
+    * `Github issues <https://github.com/biothings/mygene.info/issues>`_
+    * on twitter `@mygeneinfo <https://twitter.com/mygeneinfo>`_
+    * Post a question on `BioStars.org <https://www.biostars.org/p/new/post/?tag_val=mygene>`_ with tag #mygene.
+
+
+