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.. image:: https://pepy.tech/badge/mygene :target: https://pepy.tech/project/mygene
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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.
FAQs
Python Client for MyGene.Info services.
We found that mygene demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
Did you know?
Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.
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