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

To use HTSeq you will need:

• Python 2.7or Python >= 3.4 (tested up to 3.6)
• 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.

Both Linux and OSX are supported and binaries are provided for virtually all Linux versions and for some OSX versions (the latter only for Python 2.7 and 3.6). A source package which should not require Cython nor SWIG is provided for all other cases.

Windows is not officially supported as we don't have access to a Continuous Integration Windows machine that supports pysam. However, if you have built HTSeq for Windows, please open an issue and we'll try and include it in the release.

To install directly from PyPI:

pip install HTSeq

To install a specific version (e.g. version 0.11.0):

pip install 'HTSeq==0.11.0'

If this fails, please install all dependencies first:

pip install 'matplotlib>=1.4'
pip install Cython
pip install 'pysam>=0.9'
pip install HTSeq

NOTE: pysam==0.9.0 has a bug so that pip Cython is required at installation. pysam>=0.10.0 should build without Cython.

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

To install HTSeq itself, run:

python setup.py build install

Please see:

http://htseq.readthedocs.io