HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

NOTE: htseq is currently undergoing a major update. The master (python2.7) and python3 (python>=3.4) branches on github require pysam>=0.9, but the PyPI version refers to the last stable release, which is only compatible with pysam<=0.8.0.We will update the PyPI version within the next few weeks (hopefully!).

To use HTSeq you will need:

• Python ==2.7 (see the python3 branch for Python 3 support)
• numpy
• pysam >= 0.9.0

To run the htseq-qa script, you will also need:

• matplotlib >=1.4

To build the package from source, you will also need:

• Cython
• SWIG >=3.0.8

The latter packages are not required if you have already built HTSeq and are transferring the binaries onto another machine with a compatible environment (architechture, shared libraries). If you are not sure, chances are you need them.

Install all runtime and build dependencies. Because setuptools has historic issues with cython and optional dependencies, you need to install them before anything.

pip install Cython
pip install 'matplotlib>=1.4'

To install HTSeq itself, you can download the source from github and run:

pip install .

or install directly from PyPI (once the new version becomes available):

pip install HTSeq

Install the dependencies with your favourite tool (pip, conda, etc.).

To install HTSeq itself, run:

python setup.py build install

Please see:

http://www-huber.embl.de/users/anders/HTSeq/