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Intro
=====
*biothings_client* is an easy-to-use Python wrapper to access any Biothings.api_
-based backend service. Currently, the following clients are available:
* gene - The client for MyGene.Info_, which provides access to gene objects.
* variant - The client MyVariant.Info_, which provides access to genetic variant objects.
* chem - The client for MyChem.Info_, which provides access to chemical/drug objects.
* disease - The client for MyDisease.Info_, which provides access to disease objects.
* geneset - The client for MyGeneset.Info_, which provides access to geneset/pathway objects.
* taxon - The client for t.biothings.io_, which provides access to taxon objects.
.. _t.biothings.io: https://t.biothings.io
.. _Biothings.api: https://biothings.io
.. _MyGene.Info: https://mygene.info
.. _MyVariant.Info: https://myvariant.info
.. _MyChem.Info: https://mychem.info
.. _MyDisease.Info: https://mydisease.info
.. _MyGeneset.Info: https://mygeneset.info
.. _requests: https://pypi.python.org/pypi/requests
Requirements
============
python >=2.7 (including all python3 versions)
(It may still work under python 2.6, but it's not supported any more.)
requests_ (install using "pip install requests")
Optional dependencies
======================
* `pandas <http://pandas.pydata.org>`_ (install using "pip install pandas") is required for returning a list of variant objects as `DataFrame <http://pandas.pydata.org/pandas-docs/stable/dsintro.html#dataframe>`_.
* `requests_cache <https://pypi.python.org/pypi/requests-cache>`_ (install using "pip install requests_cache") is required for local caching of API requests.
Installation
=============
Option 1
::
pip install biothings_client
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/biothings_client.py#egg=biothings_client
Version history
===============
`CHANGES.txt <https://raw.githubusercontent.com/biothings/biothings_client.py/master/CHANGES.txt>`_
Tutorial
=========
See the `quick start tutorial <https://biothings-clientpy.readthedocs.io/en/latest/doc/Quick-Start.html>`_ at the `biothings_client doc page <https://biothings-clientpy.readthedocs.io/en/latest/index.html>`_.
Documentation
=============
https://biothings-clientpy.readthedocs.io
Usage
=====
.. code-block:: python
In [1]: from biothings_client import get_client
# get a client for variant objects
In [2]: mv = get_client("variant")
In [3]: mv.getvariant("chr7:g.140453134T>C")
Out[3]: #output below is collapsed
{"_id": "chr7:g.140453134T>C",
"_version": 1,
"chrom": "7",
"cadd": {...},
"clinvar": {...},
"cosmic": {...},
"dbnsfp": {...},
"dbsnp": {...},
"docm": {...},
"hg19": {'end': 140453134, 'start': 140453134},
"mutdb": {...},
"snpeff": {...},
"vcf": {
"alt": "C",
"position": "140453134",
"ref": "T"
}}
# get a client for gene objects
In [7]: mg = get_client("gene")
In [8]: mg.getgene(1017, 'name,symbol,refseq')
Out[8]:
{'_id': '1017',
'_score': 21.03413,
'name': 'cyclin dependent kinase 2',
'refseq': {'genomic': ['NC_000012.12', 'NC_018923.2', 'NG_034014.1'],
'protein': ['NP_001277159.1',
'NP_001789.2',
'NP_439892.2',
'XP_011536034.1'],
'rna': ['NM_001290230.1', 'NM_001798.4', 'NM_052827.3', 'XM_011537732.1'],
'translation': [{'protein': 'NP_001789.2', 'rna': 'NM_001798.4'},
{'protein': 'NP_439892.2', 'rna': 'NM_052827.3'},
{'protein': 'NP_001277159.1', 'rna': 'NM_001290230.1'},
{'protein': 'XP_011536034.1', 'rna': 'XM_011537732.1'}]},
'symbol': 'CDK2'}
# get a client for chems/drugs
In [9]: md = get_client("chem")
In [10]: md.getchem("ATBDZSAENDYQDW-UHFFFAOYSA-N", fields="pubchem")
Out[10]:
{'_id': 'ATBDZSAENDYQDW-UHFFFAOYSA-N',
'_version': 1,
'pubchem': {'chiral_atom_count': 0,
'chiral_bond_count': 0,
'cid': 'CID4080429',
'complexity': 250,
'covalently-bonded_unit_count': 1,
'defined_atom_stereocenter_count': 0,
'defined_bond_stereocenter_count': 0,
'exact_mass': 184.019415,
'formal_charge': 0,
'heavy_atom_count': 12,
'hydrogen_bond_acceptor_count': 3,
'hydrogen_bond_donor_count': 1,
'inchi': 'InChI=1S/C8H8O3S/c1-2-7-4-3-5-8(6-7)12(9,10)11/h2-6H,1H2,(H,9,10,11)',
'inchi_key': 'ATBDZSAENDYQDW-UHFFFAOYSA-N',
'isotope_atom_count': 0,
'iupac': {'traditional': '3-vinylbesylic acid'},
'molecular_formula': 'C8H8O3S',
'molecular_weight': 184.21232,
'monoisotopic_weight': 184.019415,
'rotatable_bond_count': 2,
'smiles': {'isomeric': 'C=CC1=CC(=CC=C1)S(=O)(=O)O'},
'tautomers_count': 1,
'topological_polar_surface_area': 62.8,
'undefined_atom_stereocenter_count': 0,
'undefined_bond_stereocenter_count': 0,
'xlogp': 1.4}}
# get a client for taxa
In [11]: mt = get_client("taxon")
In [12]: mt.gettaxon(9606)
Out[12]:
{'_id': '9606',
'_version': 1,
'authority': ['homo sapiens linnaeus, 1758'],
'common_name': 'man',
'genbank_common_name': 'human',
'has_gene': True,
'lineage': [9606,
9605,
207598,
9604,
314295,
9526,
314293,
376913,
9443,
314146,
1437010,
9347,
32525,
40674,
32524,
32523,
1338369,
8287,
117571,
117570,
7776,
7742,
89593,
7711,
33511,
33213,
6072,
33208,
33154,
2759,
131567,
1],
'other_names': ['humans'],
'parent_taxid': 9605,
'rank': 'species',
'scientific_name': 'homo sapiens',
'taxid': 9606,
'uniprot_name': 'homo sapiens'}
Contact
========
Drop us any feedback `@biothingsapi <https://twitter.com/biothingsapi>`_
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"description": ".. image:: https://badge.fury.io/py/biothings-client.svg\n :target: https://pypi.python.org/pypi/biothings-client\n\n.. image:: https://img.shields.io/pypi/pyversions/biothings-client.svg\n :target: https://pypi.python.org/pypi/biothings-client\n\n.. image:: https://img.shields.io/pypi/format/biothings-client.svg\n :target: https://pypi.python.org/pypi/biothings-client\n\n.. image:: https://github.com/biothings/biothings_client.py/actions/workflows/build-package.yml/badge.svg\n :target: https://github.com/biothings/biothings_client.py/actions/workflows/build-package.yml\n\n.. image:: https://github.com/biothings/biothings_client.py/actions/workflows/run-tests.yml/badge.svg\n :target: https://github.com/biothings/biothings_client.py/actions/workflows/run-tests.yml\n\n.. image:: https://api.codacy.com/project/badge/Grade/2b716becb6e948a6b576f278e64dd81f\n :alt: Codacy Badge\n :target: https://www.codacy.com/gh/biothings/biothings_client.py/dashboard?utm_source=github.com&utm_medium=referral&utm_content=biothings/biothings_client.py&utm_campaign=Badge_Grade\n\n.. image:: https://app.codacy.com/project/badge/Coverage/2b716becb6e948a6b576f278e64dd81f\n :alt: Codacy Coverage Badge\n :target: https://app.codacy.com/gh/biothings/biothings_client.py/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage\n\n.. image:: https://img.shields.io/pypi/dm/biothings_client.svg\n :alt: PyPI Downloads\n :target: https://pypistats.org/packages/biothings_client\n\n.. image:: https://readthedocs.org/projects/biothings-clientpy/badge/?version=latest\n :alt: Documentation Status\n :target: https://biothings-clientpy.readthedocs.io/en/latest/?badge=latest\n\nIntro\n=====\n\n*biothings_client* is an easy-to-use Python wrapper to access any Biothings.api_\n-based backend service. Currently, the following clients are available:\n\n * gene - The client for MyGene.Info_, which provides access to gene objects.\n * variant - The client MyVariant.Info_, which provides access to genetic variant objects.\n * chem - The client for MyChem.Info_, which provides access to chemical/drug objects.\n * disease - The client for MyDisease.Info_, which provides access to disease objects.\n * geneset - The client for MyGeneset.Info_, which provides access to geneset/pathway objects.\n * taxon - The client for t.biothings.io_, which provides access to taxon objects.\n\n.. _t.biothings.io: https://t.biothings.io\n.. _Biothings.api: https://biothings.io\n.. _MyGene.Info: https://mygene.info\n.. _MyVariant.Info: https://myvariant.info\n.. _MyChem.Info: https://mychem.info\n.. _MyDisease.Info: https://mydisease.info\n.. _MyGeneset.Info: https://mygeneset.info\n.. _requests: https://pypi.python.org/pypi/requests\n\nRequirements\n============\n python >=2.7 (including all python3 versions)\n\n (It may still work under python 2.6, but it's not supported any more.)\n\n requests_ (install using \"pip install requests\")\n\nOptional dependencies\n======================\n * `pandas <http://pandas.pydata.org>`_ (install using \"pip install pandas\") is required for returning a list of variant objects as `DataFrame <http://pandas.pydata.org/pandas-docs/stable/dsintro.html#dataframe>`_.\n * `requests_cache <https://pypi.python.org/pypi/requests-cache>`_ (install using \"pip install requests_cache\") is required for local caching of API requests.\n\nInstallation\n=============\n\n Option 1\n ::\n\n pip install biothings_client\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/biothings_client.py#egg=biothings_client\n\nVersion history\n===============\n\n `CHANGES.txt <https://raw.githubusercontent.com/biothings/biothings_client.py/master/CHANGES.txt>`_\n\nTutorial\n=========\n\n See the `quick start tutorial <https://biothings-clientpy.readthedocs.io/en/latest/doc/Quick-Start.html>`_ at the `biothings_client doc page <https://biothings-clientpy.readthedocs.io/en/latest/index.html>`_.\n\nDocumentation\n=============\n\n https://biothings-clientpy.readthedocs.io\n\nUsage\n=====\n\n.. code-block:: python\n\n In [1]: from biothings_client import get_client\n\n # get a client for variant objects\n\n In [2]: mv = get_client(\"variant\")\n\n In [3]: mv.getvariant(\"chr7:g.140453134T>C\")\n Out[3]: #output below is collapsed\n {\"_id\": \"chr7:g.140453134T>C\",\n \"_version\": 1,\n \"chrom\": \"7\",\n \"cadd\": {...},\n \"clinvar\": {...},\n \"cosmic\": {...},\n \"dbnsfp\": {...},\n \"dbsnp\": {...},\n \"docm\": {...},\n \"hg19\": {'end': 140453134, 'start': 140453134},\n \"mutdb\": {...},\n \"snpeff\": {...},\n \"vcf\": {\n \"alt\": \"C\",\n \"position\": \"140453134\",\n \"ref\": \"T\"\n }}\n\n # get a client for gene objects\n\n In [7]: mg = get_client(\"gene\")\n\n In [8]: mg.getgene(1017, 'name,symbol,refseq')\n Out[8]:\n {'_id': '1017',\n '_score': 21.03413,\n 'name': 'cyclin dependent kinase 2',\n 'refseq': {'genomic': ['NC_000012.12', 'NC_018923.2', 'NG_034014.1'],\n 'protein': ['NP_001277159.1',\n 'NP_001789.2',\n 'NP_439892.2',\n 'XP_011536034.1'],\n 'rna': ['NM_001290230.1', 'NM_001798.4', 'NM_052827.3', 'XM_011537732.1'],\n 'translation': [{'protein': 'NP_001789.2', 'rna': 'NM_001798.4'},\n {'protein': 'NP_439892.2', 'rna': 'NM_052827.3'},\n {'protein': 'NP_001277159.1', 'rna': 'NM_001290230.1'},\n {'protein': 'XP_011536034.1', 'rna': 'XM_011537732.1'}]},\n 'symbol': 'CDK2'}\n\n # get a client for chems/drugs\n\n In [9]: md = get_client(\"chem\")\n\n In [10]: md.getchem(\"ATBDZSAENDYQDW-UHFFFAOYSA-N\", fields=\"pubchem\")\n Out[10]:\n {'_id': 'ATBDZSAENDYQDW-UHFFFAOYSA-N',\n '_version': 1,\n 'pubchem': {'chiral_atom_count': 0,\n 'chiral_bond_count': 0,\n 'cid': 'CID4080429',\n 'complexity': 250,\n 'covalently-bonded_unit_count': 1,\n 'defined_atom_stereocenter_count': 0,\n 'defined_bond_stereocenter_count': 0,\n 'exact_mass': 184.019415,\n 'formal_charge': 0,\n 'heavy_atom_count': 12,\n 'hydrogen_bond_acceptor_count': 3,\n 'hydrogen_bond_donor_count': 1,\n 'inchi': 'InChI=1S/C8H8O3S/c1-2-7-4-3-5-8(6-7)12(9,10)11/h2-6H,1H2,(H,9,10,11)',\n 'inchi_key': 'ATBDZSAENDYQDW-UHFFFAOYSA-N',\n 'isotope_atom_count': 0,\n 'iupac': {'traditional': '3-vinylbesylic acid'},\n 'molecular_formula': 'C8H8O3S',\n 'molecular_weight': 184.21232,\n 'monoisotopic_weight': 184.019415,\n 'rotatable_bond_count': 2,\n 'smiles': {'isomeric': 'C=CC1=CC(=CC=C1)S(=O)(=O)O'},\n 'tautomers_count': 1,\n 'topological_polar_surface_area': 62.8,\n 'undefined_atom_stereocenter_count': 0,\n 'undefined_bond_stereocenter_count': 0,\n 'xlogp': 1.4}}\n\n # 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