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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
Support
============
python >=3.7
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>`_.
Installation
=============
* Option 1. Install from pypi repository using pip:
.. code-block:: bash
pip install biothings_client
* Option 2. Install the latest commit from the github repository using pip:
.. code-block:: bash
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
=====
* Synchronous client.
.. code-block:: python
from biothings_client import get_client
# get a client for variant objects
mv = get_client("variant")
mv.getvariant("chr7:g.140453134T>C")
# 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
mg = get_client("gene")
mg.getgene(1017, 'name,symbol,refseq')
{'_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
md = get_client("chem")
md.getchem("ATBDZSAENDYQDW-UHFFFAOYSA-N", fields="pubchem")
{'_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
mt = get_client("taxon")
mt.gettaxon(9606)
{'_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'}
* Asynchronous client.
.. code-block:: python
from biothings_client import get_async_client
# get a client for variant objects
mv = get_async_client("variant")
await mv.getvariant("chr7:g.140453134T>C")
# get a client for gene objects
mg = get_async_client("gene")
await mg.getgene(1017, 'name,symbol,refseq')
# get a client for chems/drugs
md = get_async_client("chem")
await md.getchem("ATBDZSAENDYQDW-UHFFFAOYSA-N", fields="pubchem")
# get a client for taxa
mt = get_async_client("taxon")
await mt.gettaxon(9606)
Contact
========
Drop us any feedback `@biothingsapi <https://twitter.com/biothingsapi>`_
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"author": "Cyrus Afrasiabi, Xinghua Zhou",
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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\nSupport\n============\n python >=3.7\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\nInstallation\n=============\n\n\n * Option 1. Install from pypi repository using pip:\n\n .. code-block:: bash\n\n pip install biothings_client\n\n\n * Option 2. Install the latest commit from the github repository using pip:\n \n .. code-block:: bash\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* Synchronous client.\n\n .. code-block:: python\n\n from biothings_client import get_client\n\n # get a client for variant objects\n mv = get_client(\"variant\")\n\n mv.getvariant(\"chr7:g.140453134T>C\")\n\n # 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 mg = get_client(\"gene\")\n\n mg.getgene(1017, 'name,symbol,refseq')\n\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 md = get_client(\"chem\")\n\n md.getchem(\"ATBDZSAENDYQDW-UHFFFAOYSA-N\", fields=\"pubchem\")\n\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 # get a client for taxa\n mt = get_client(\"taxon\")\n\n mt.gettaxon(9606)\n\n {'_id': '9606',\n '_version': 1,\n 'authority': ['homo sapiens linnaeus, 1758'],\n 'common_name': 'man',\n 'genbank_common_name': 'human',\n 'has_gene': True,\n 'lineage': [9606,\n 9605,\n 207598,\n 9604,\n 314295,\n 9526,\n 314293,\n 376913,\n 9443,\n 314146,\n 1437010,\n 9347,\n 32525,\n 40674,\n 32524,\n 32523,\n 1338369,\n 8287,\n 117571,\n 117570,\n 7776,\n 7742,\n 89593,\n 7711,\n 33511,\n 33213,\n 6072,\n 33208,\n 33154,\n 2759,\n 131567,\n 1],\n 'other_names': ['humans'],\n 'parent_taxid': 9605,\n 'rank': 'species',\n 'scientific_name': 'homo sapiens',\n 'taxid': 9606,\n 'uniprot_name': 'homo sapiens'}\n\n* Asynchronous client.\n\n .. code-block:: python\n\n from biothings_client import get_async_client\n\n # get a client for variant objects\n mv = get_async_client(\"variant\")\n await mv.getvariant(\"chr7:g.140453134T>C\")\n\n # get a client for gene objects\n mg = get_async_client(\"gene\")\n await mg.getgene(1017, 'name,symbol,refseq')\n\n # get a client for chems/drugs\n md = get_async_client(\"chem\")\n await md.getchem(\"ATBDZSAENDYQDW-UHFFFAOYSA-N\", fields=\"pubchem\")\n\n # get a client for taxa\n mt = get_async_client(\"taxon\")\n await mt.gettaxon(9606)\n\n\n\n\nContact\n========\nDrop us any feedback `@biothingsapi <https://twitter.com/biothingsapi>`_\n",
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