Metadata-Version: 1.2
Name: pronto
Version: 0.10.1
Summary: Python frontend to ontologies
Home-page: https://github.com/althonos/pronto
Author: Martin Larralde
Author-email: martin.larralde@ens-paris-saclay.fr
License: MIT
Description-Content-Type: UNKNOWN
Description: **pronto** : Python frontend to Ontologies
        ==========================================
        
        |Version| |Py versions| |Build Status| |Dev repo| |Codacy grade| |License| |DOI| |coverage| |rtd|
        
        Overview
        ^^^^^^^^
        
        Pronto is a python module to parse, create, browse and export ontologies
        from some popular formats. For now, **obo** and **owl/xml** are available,
        but more formats are to be added in the future (you can even add your
        own to work with the current API).
        
        Installation
        ^^^^^^^^^^^^
        
        Installing with pip is the easiest:
        
        .. code:: bash
        
            pip install pronto          # if you have the admin rights
            pip install pronto --user   # if you want to install it for only one user
        
        If for some reason you do not like ``pip``, you can also clone the
        repository and install it with the setup script (still requires
        ``setuptools``):
        
        .. code:: bash
        
            git clone https://github.com/althonos/pronto
            cd pronto
            python setup.py install    # may also require admin rights
        
        Usage
        ^^^^^
        
        The ``Ontology`` class is the main entrypoint of ``pronto``. It can
        be instantiated with a given ontology file (``.owl``, ``.ont`` or ``.obo``)
        or from scratch, without any existing terms.
        
        Open an ontology and get a term by accession:
        '''''''''''''''''''''''''''''''''''''''''''''
        
        .. code:: python
        
            import pronto
            ont = pronto.Ontology('path/to/file.obo')
            term = ont['REF:ACCESSION']
        
        Display an ontology in obo format and in json format:
        '''''''''''''''''''''''''''''''''''''''''''''''''''''
        
        .. code:: python
        
            import pronto
            ont = pronto.Ontology('https://net.path.should/work/too.owl')
            print(ont.obo)
            print(ont.json)
        
        Merge two ontologies:
        '''''''''''''''''''''
        
        Example here uses the `NMR controlled vocabulary <http://nmrml.org/cv/>`_ and the
        `HUPO-PSI MS controlled vocabulary <http://www.psidev.info/groups/controlled-vocabularies>`_
        
        .. code:: python
        
            import pronto
            nmr = pronto.Ontology('http://nmrml.org/cv/v1.1.0/nmrCV.owl')
            ms  = pronto.Ontology('https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo')
            ms.merge(nmr)
        
        .. code:: python
        
            >>> 'NMR:1000004' in ms
            True
            >>> ms.meta['coverage']
            'Mass spectrometer output files and spectra interpretation'
        
        
        Find ontology terms with children
        '''''''''''''''''''''''''''''''''
        
        .. code:: python
        
            import pronto
            ont = pronto.Ontology('path/to/file.obo')
            for term in ont:
                if term.children:
                    print(term)
        
        
        Get all the transitive children of an ontology term
        '''''''''''''''''''''''''''''''''''''''''''''''''''
        
        .. code:: python
        
            import pronto
            ont = pronto.Ontology('path/to/file.obo')
            print(ont['RF:XXXXXXX'].rchildren())
        
        
        Reference
        ^^^^^^^^^
        
        If you wish to use this library in a scientific publication,
        please cite it !
        (see the `Zenodo record <https://zenodo.org/badge/latestdoi/23304/althonos/pronto>`_
        to get a DOI or a BibTEX record).
        
        
        .. |Build Status| image:: https://img.shields.io/travis/althonos/pronto.svg?style=flat&maxAge=3600
           :target: https://travis-ci.org/althonos/pronto
        
        .. |Py versions| image:: https://img.shields.io/pypi/pyversions/pronto.svg?style=flat&maxAge=3600
           :target: https://pypi.python.org/pypi/pronto/
        
        .. |Version| image:: https://img.shields.io/pypi/v/pronto.svg?style=flat&maxAge=3600
           :target: https://pypi.python.org/pypi/pronto
        
        .. |Dev repo| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
           :target: https://github.com/althonos/pronto
        
        .. |License| image:: https://img.shields.io/pypi/l/pronto.svg?style=flat&maxAge=3600
           :target: https://choosealicense.com/licenses/mit/
        
        .. |Codacy Grade| image:: https://img.shields.io/codacy/grade/157b5fd24e5648ea80580f28399e79a4.svg?style=flat&maxAge=3600
           :target: https://codacy.com/app/althonos/pronto
        
        .. |DOI| image:: https://zenodo.org/badge/62424052.svg
           :target: https://zenodo.org/badge/latestdoi/62424052
        
        .. |coverage| image:: https://img.shields.io/codacy/coverage/157b5fd24e5648ea80580f28399e79a4.svg?maxAge=3600
           :target: https://www.codacy.com/app/althonos/pronto/dashboard
        
        .. |rtd| image:: https://readthedocs.org/projects/pronto/badge/?version=latest
           :target: http://pronto.readthedocs.io/en/latest/?badge=latest
           :alt: Documentation Status
        
Keywords: Bio-Informatics,Ontology,OBO,Owl,convert,parse
Platform: any
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Operating System :: OS Independent
Requires-Python: >= 2.7, != 3.0.*, != 3.1.*, != 3.2.*
