Metadata-Version: 1.1
Name: pronto
Version: 0.6.2
Summary: Python frontend to ontologies - a library to parse, create, browse and export ontologies.
Home-page: http://github.com/althonos/pronto
Author: Martin Larralde
Author-email: martin.larralde@ens-cachan.fr
License: GPLv3
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
            python3 setup.py install    # may also require admin rights
        
        Usage
        ^^^^^
        
        The class Ontology is likely the one you'll use the most
        if all you want is to browse ontologies. It can be used to import 
        ontologies in .owl (sometimes seen as .ont) and .obo formats,
        merge, and export ontologies to a rudimentary obo file.
        
        Instantiate an obo ontology and getting a term by accession number:
        
        .. 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:
        
        .. code:: python
        
            import pronto
            nmr = pronto.Ontology('https://raw.githubusercontent.com/nmrML/nmrML/'
                                  'master/ontologies/nmrCV.owl')
            ms  = pronto.Ontology('http://psidev.cvs.sourceforge.net/viewvc/psidev/psi'
                                  '/psi-ms/mzML/controlledVocabulary/psi-ms.obo')
        
            ms.merge(nmr) # MS ontology keeps its metadata but now contains NMR terms
                          # as well.
        
            assert('NMR:1000004' in ms)
        
        Explore every term of an ontology and print those with children:
        
        .. code:: python
        
            import pronto
            ont = pronto.Ontology('path/to/file.obo')
            for term in ont:
                if term.children:
                    print(term)
        
        Get grandchildrens of an ontology term:
        
        .. code:: python
        
            import pronto
            ont = pronto.Ontology('path/to/file.obo')
            print(ont['RF:XXXXXXX'].children.children)
        
        TODO
        ^^^^
        -  test with many different ontologies
        -  extract data from OwlXML where attributes are ontologic terms
        -  extract metadatas from OwlXML
        -  add other owl serialized formats
        -  (maybe) add serialization to owl
        
        
        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>`__).
        
        Author: Martin Larralde
        
        
        .. |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://www.gnu.org/licenses/gpl-3.0.html
        
        .. |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/23304/althonos/pronto.svg
           :target: https://zenodo.org/badge/latestdoi/23304/althonos/pronto
        
        .. |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: 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 :: 3.2
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Interface Engine/Protocol Translator
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Operating System :: OS Independent
