A library of python functions and classes to assist in processing high-throughput biological data

pip install pyokit==0.2.0


Pyokit: Python Bio Toolkit

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Pyokit is a python library with a collection of tools to make the processing and analysis of high-throughput biological datasets in python easier.


Pyokit depends on rpy2 for some of its functionality. You don't strictly need it, Pyokit can be installed without it, but if you don't have it some functionality will not be supported.


From PyPI. Pyokit is available from the Python package index. The easiest way to install it is to use pip. Note that you may need to prefix certain commands below with sudo if you're installing to the global python installation.

  1. Get pip (if you don't already have it):

This will install pip for you. if python doesn't point to the version of python you want to use, then replace it with the full path to the one you prefer (you'll probably have to do that if you don't have admin. access on the machine you're using).
2. Now you can install pyokit:

pip install pyokit

... and you're done.

From source. The bleeding-edge version can always be cloned from the GitHub repository (, where tagged releases can also be downloaded as .tar.gz. If you take this route, you will still need pip (see above if you don't have it). After unpacking the distribution (or cloning the repository), cd into the newly created directory and then

  1. Build the distribution package:
python sdist
  1. Install the distribution:
pip install --no-index dist/pyokit-a.b.c.tar.gz

where a.b.c is the version you downloaded.

Using Pyokit

Everything you need to know should be in the Pyokit manual. You can find it here:

Contacts and bug reports

Philip J. Uren

If you found a bug or mistake in this project, I would like to know about it. Before you send me the bug report though, please check the following:

  1. Are you using the latest version? The bug you found may already have been fixed.
  2. Check that your input is in the correct format and you have selected the correct options.
  3. Please reduce your input to the smallest possible size that still produces the bug; I will need your input data to reproduce the problem, and the smaller you can make it, the easier it will be for both of us.

License information

The following applys to this software package and all subparts therein

Pyokit Copyright (C) 2014 Philip J. Uren

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA