pronto 0.10.0

Python frontend to ontologies - a library to parse, create,

browse and export ontologies
Home-page: https://github.com/althonos/pronto
Author: Martin Larralde
Author-email: [e-mail]
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.*