Metadata-Version: 2.0
Name: pronto
Version: 0.1.1
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 : **P**ython f**ron**tend **t**o **O**ntologies

[![Build Status (Py2.7 and Py3.5)](https://travis-ci.org/althonos/pronto.svg?branch=master)](https://travis-ci.org/althonos/pronto)

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

Display an ontology in obo format and in json format:
```python
import pronto
ont = pronto.OwlXML('https://net.path.should/work/too.owl')
print(ont.obo)
print(ont.json)
```

Merge two ontologies:
```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:
```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:
```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



