Metadata-Version: 2.0
Name: pronto
Version: 0.1.2
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
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 :: 3.3
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
Requires-Dist: lxml
Provides-Extra: doc
Requires-Dist: Sphinx; extra == 'doc'
Requires-Dist: sphinx-rtd-theme; extra == 'doc'

**pronto** : Python frontend to Ontologies
==========================================

|Version| |Build Status| |Py versions| |License|

Overview
^^^^^^^^

pronto is a python module to parse, create, browse and export ontologies
from some popular formats. For now, **obo** and **owl/xml** were added,
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
^^^^^

Currently there are 2 classes which both inherit from Ontology: **Obo**
and **OwlXML**. To parse the right kind of file you have to use the
right class, although that will probably change to the future to provide
an unique **Ontology** class. Right now though you can still use the
Ontology class as a base to merge other ontologies into.

Instantiate an obo ontology and getting a term by accession number:

.. code:: python

    import pronto
    ont = pronto.Obo('path/to/file.obo')
    term = ont['REF:ACCESSION']

Display an ontology in obo format and in json format:

.. code:: python

    import pronto
    ont = pronto.OwlXML('https://net.path.should/work/too.owl')
    print(ont.obo)
    print(ont.json)

Merge two ontologies:

.. code:: python

    import pronto
    nmr = pronto.OwlXML('https://raw.githubusercontent.com/nmrML/nmrML/'
                        'master/ontologies/nmrCV.owl')
    ms  =    pronto.Obo('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.Obo('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.Obo('path/to/file.obo')
    print(ont['RF:XXXXXXX'].children.children)

TODO
^^^^

-  redefine OwlXML and Obo as Parsers in pronto.parser, and always use
   Ontology to open an ontology file.
-  properly define Import Warnings whenever an import fails.
-  write a proper documentation
-  create a proper relationship class
-  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

.. |Build Status| image:: https://travis-ci.org/althonos/pronto.svg?branch=master&style=flat
   :target: https://travis-ci.org/althonos/pronto

.. |Py versions| image:: https://img.shields.io/pypi/pyversions/pronto.svg?style=flat
   :target: https://pypi.python.org/pypi/pronto/

.. |Version| image:: https://img.shields.io/pypi/version/pronto.svg?style=flat

.. |License| image:: https://img.shields.io/pypi/l/pronto.svg   
   :target: https://www.gnu.org/licenses/gpl-3.0.html


