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Working with wiggle tracks in Python

Project description

Working with wiggle tracks in Python.

Wiggelen is a Python library for working with wiggle tracks (WIG files). It also provides a command line interface to some of its functionality.

The main goal of Wiggelen is to provide light-weight and unified access to wiggle tracks.

>>> import wiggelen
>>> for x in wiggelen.walk(open('test.wig')):
...     print 'chr%s:%d\t%s' % x
...
chr18:34344  629.0
chr18:34345  649.0
chr18:34446  657.0
chrM:308     520.0
chrM:309     519.0

Installation

The Wiggelen source code is hosted on GitHub. Supported Python versions for running Wiggelen are 2.6, 2.7, 3.2, 3.3, and PyPy (unit tests are run automatically on these platforms using the Travis CI service).

Wiggelen can be installed either via the Python Package Index (PyPi) or from the source code.

Latest release via PyPi

To install the latest release via PyPi using pip:

pip install wiggelen

Development version

You can also clone and use the latest development version directly from the GitHub repository:

git clone https://github.com/martijnvermaat/wiggelen.git
cd wiggelen
python setup.py install

Documentation

The latest documentation including a user’s guide and API reference is hosted at Read The Docs.

You can also compile the documentation directly from the source code by running make html from the doc/ subdirectory. This requires Sphinx to be installed.

Project details


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