Metadata-Version: 2.1
Name: pyobo
Version: 0.2.1
Summary: Handling and writing OBO
Home-page: https://github.com/pyobo/pyobo
Author: Charles Tapley Hoyt
Author-email: cthoyt@gmail.com
Maintainer: Charles Tapley Hoyt
Maintainer-email: cthoyt@gmail.com
License: MIT
Download-URL: https://github.com/pyobo/pyobo/releases
Project-URL: Bug Tracker, https://github.com/pyobo/pyobo/issues
Project-URL: Source Code, https://github.com/pyobo/pyobo
Description: PyOBO |build|
        =============
        Tools for biological identifiers, names, synonyms, xrefs, hierarchies, relations, and properties through the
        perspective of OBO.
        
        Example Usage
        -------------
        Note! PyOBO is no nonsense. This means that there's no repetitive
        prefixes in identifiers. It also means all identifiers are strings,
        no exceptions.
        
        Note! The first time you run these, they have to download and cache
        all resources. We're not in the business of redistributing data,
        so all scripts should be completely reproducible. There's some
        AWS tools for hosting/downloading pre-compiled versions in
        ``pyobo.aws`` if you don't have time for that.
        
        Get mapping of ChEBI identifiers to names.
        
        .. code-block:: python
        
           import pyobo
        
           chebi_id_to_name = pyobo.get_id_name_mapping('chebi')
        
           name = chebi_id_to_name['132964']
           assert name == 'fluazifop-P-butyl'
        
        Or, you don't have time for two lines
        
        .. code-block:: python
        
            import pyobo
        
            name = pyobo.get_name('chebi', '132964')
            assert name == 'fluazifop-P-butyl'
        
        Get reverse mapping of ChEBI names to identifiers
        
        .. code-block:: python
        
            import pyobo
        
            chebi_name_to_id = pyobo.get_name_id_mapping('chebi')
        
            identifier = chebi_name_to_id['fluazifop-P-butyl']
            assert identifier == '132964'
        
        Maybe you live in CURIE world and just want to normalize something like
        `CHEBI:132964`:
        
        .. code-block:: python
        
            import pyobo
        
            name = pyobo.get_name_by_curie('CHEBI:132964')
            assert name == 'fluazifop-P-butyl'
        
        
        Maybe you've got names/synonyms you want to try and map back to ChEBI synonyms.
        Given the brand name `Fusilade II` of `CHEBI:132964`, it should be able to look
        it up and its preferred label.
        
        .. code-block:: python
        
            import pyobo
        
            prefix, identifier, name = pyobo.ground('chebi', 'Fusilade II')
            assert prefix == 'chebi'
            assert identifier == '132964'
            assert name == 'fluazifop-P-butyl'
        
            # When failure happens...
            prefix, identifier, name = pyobo.ground('chebi', 'Definitely not a real name')
            assert prefix is None
            assert identifier is None
            assert name is None
        
        
        Get xrefs from ChEBI to PubChem
        
        .. code-block:: python
        
            import pyobo
        
            chebi_id_to_pubchem_compound_id = pyobo.get_filtered_xrefs('chebi', 'pubchem.compound')
        
            pubchem_compound_id = chebi_id_to_pubchem_compound_id['132964']
            assert pubchem_compound_id == '3033674'
        
        Get properties, like SMILES. The semantics of these are defined on an OBO-OBO basis.
        
        .. code-block:: python
        
            import pyobo
        
            # I dont make the rules. I wouldn't have chosen this as the key for this property. It could be any string
            chebi_smiles_property = 'http://purl.obolibrary.org/obo/chebi/smiles'
            chebi_id_to_smiles = pyobo.get_filtered_properties_mapping('chebi', chebi_smiles_property)
        
            smiles = chebi_id_to_smiles['132964']
            assert smiles == 'C1(=CC=C(N=C1)OC2=CC=C(C=C2)O[C@@H](C(OCCCC)=O)C)C(F)(F)F'
        
        Installation |pypi_version| |python_versions| |pypi_license|
        ------------------------------------------------------------
        PyOBO can be installed from `PyPI <https://pypi.org/project/pyobo/>`_ with:
        
        .. code-block:: sh
        
            $ pip install pyobo
        
        It can be installed in development mode from `GitHub <https://github.com/pyobo/pyobo>`_
        with:
        
        .. code-block:: sh
        
            $ git clone https://github.com/pyobo/pyobo.git
            $ cd pyobo
            $ pip install -e .
        
        .. |build| image:: https://travis-ci.com/pyobo/pyobo.svg?branch=master
            :target: https://travis-ci.com/pyobo/pyobo
            :alt: Build Status
        
        .. |coverage| image:: https://codecov.io/gh/pyobo/pyobo/coverage.svg?branch=master
            :target: https://codecov.io/gh/pyobo/pyobo?branch=master
            :alt: Coverage Status
        
        .. |docs| image:: http://readthedocs.org/projects/pyobo/badge/?version=latest
            :target: http://pyobo.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
        .. |python_versions| image:: https://img.shields.io/pypi/pyversions/pyobo.svg
            :alt: Stable Supported Python Versions
        
        .. |pypi_version| image:: https://img.shields.io/pypi/v/pyobo.svg
            :alt: Current version on PyPI
        
        .. |pypi_license| image:: https://img.shields.io/pypi/l/pyobo.svg
            :alt: MIT License
        
Keywords: Open Biomedical Ontologies,OBO
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.7
Provides-Extra: docs
Provides-Extra: web
