Metadata-Version: 2.1
Name: biothings-client
Version: 0.2.5
Summary: Python Client for BioThings API services.
Home-page: https://github.com/biothings/biothings_client.py
Author: Cyrus Afrasiabi, Xinghua Zhou, Chunlei Wu
Author-email: cwu@scripps.edu
License: BSD
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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.
            * taxon - The client for t.biothings.io_, which provides access to taxon objects.
        
        .. _t.biothings.io: http://t.biothings.io
        .. _Biothings.api: http://biothings.io
        .. _MyGene.Info: http://mygene.info
        .. _MyVariant.Info: http://myvariant.info
        .. _MyChem.Info: http://mychem.info
        .. _MyDisease.Info: http://mydisease.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>`_
        
Keywords: biology variant gene taxon species drug annotation web service client api myvariant mygene
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 :: 4 - Beta
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
Provides-Extra: caching
Provides-Extra: dataframe
Provides-Extra: jsonld
