gprofiler-official 0.3

Functional enrichment analysis and more via the g:Profiler toolkit

The official Python 3 interface to the g:Profiler [1] toolkit for enrichment analysis of functional (GO and other) terms, conversion between identifier namespaces and mapping orhologous genes in related organisms. This library provides both a command-line tool and a Python module. It is designed to be lightweight and not require any 3rd party packages.

Besides this README, the API documentation is available [6].

Note that this used to be a Python 2 module. Since version 0.3, it has been migrated to Python 3. Please use archived versions in case you require Python 2 support.

Installation on Linux using pip

The pip tool [4] is the recommended method of installing Python packages.

Optionally create a virtual environment [2]:

$ virtualenv myenv
$ source myenv/bin/activate

Install the software with pip, see [3] for instructions:

$ pip install gprofiler-official

Make sure that the installed gprofiler.py script is on your $PATH. When using a virtual environment as shown above, this should happen automatically.

Run an example query:

$ gprofiler.py -o scerevisiae "swi4 swi6"

For detailed usage instructions, see:

$ gprofiler.py --help

To use the module in your codebase:

from gprofiler import GProfiler
gp = GProfiler("MyToolName/0.1")
result = gp.gprofile("sox2")

For details, see the API documentation [6].

Installation on Linux using the tarball

You may simply download the tarball from gprofiler-official PyPI page [5], extract it and use the gprofiler.py script without installation. For detailed usage instructions, see:

$ gprofiler.py --help

You may run the test suite with:

$ python3 setup.py test

Installation on other platforms

Please see [3] for package installation instructions on various platforms.

• [1] http://biit.cs.ut.ee/gprofiler

• [2] http://docs.python-guide.org/en/latest/dev/virtualenvs/

• [3] https://python-packaging-user-guide.readthedocs.org/en/latest/installing/

• [4] https://pip.pypa.io/en/stable/

• [5] https://pypi.python.org/pypi/gprofiler-official

• [6] http://biit.cs.ut.ee/gprofiler_beta/doc/python/