kpgaffney / htseq

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

HTSeq

DEVS: https://github.com/htseq/htseq

DOCS: https://htseq.readthedocs.io

A Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. A popular use of HTSeq is htseq-count, a tool to quantify gene expression in RNA-Seq and similar experiments.

Requirements

To use HTSeq you will need:

• Python 2.7 or Python >= 3.5
• numpy
• pysam >= 0.9.0

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

• matplotlib >=1.4

Both Linux and OSX are supported and binaries are provided on Pypi.

A source package which should not require Cython nor SWIG is also provided on Pypi.

To develop HTSeq you will also need:

• Cython >=0.29.5
• SWIG >=3.0.8

Windows is not officially supported as we don't have access to a Continuous Integration Windows machine that supports pysam. Please do not open an issue asking to support Windows installers: we do not know how to do that and do not have the bandwidth to learn. However, if you are interested in giving it a try yourself, we are happy to provide as much support as we can.

Installation

PIP

To install directly from PyPI:

pip install HTSeq

To install a specific version:

pip install 'HTSeq==0.14.0'

If this fails, please install all dependencies first:

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

setup.py (distutils/setuptools)

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

To install HTSeq itself, run:

python setup.py build install

Authors

• Since 2016: Fabio Zanini @ http://fabilab.org.
• 2020-2015: Simon Anders, Wolfgang Huber