Metadata-Version: 2.1
Name: HTSeq
Version: 0.12.3
Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays
Home-page: https://github.com/htseq
Author: Simon Anders, Fabio Zanini
Author-email: fabio.zanini@unsw.edu.au
Maintainer: Fabio Zanini
Maintainer-email: fabio.zanini@unsw.edu.au
License: GPL3
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python
Description-Content-Type: text/markdown
Requires-Dist: numpy
Requires-Dist: pysam
Provides-Extra: htseq-qa
Requires-Dist: matplotlib (>=1.4) ; extra == 'htseq-qa'

[![Build Status](https://travis-ci.org/htseq/htseq.svg?branch=master)](https://travis-ci.org/htseq/htseq)
[![Documentation Status](https://readthedocs.org/projects/htseq/badge/?version=master)](https://htseq.readthedocs.io)

# 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:

```bash
pip install HTSeq
```

To install a specific version:

```bash
pip install 'HTSeq==0.14.0'
```

If this fails, please install all dependencies first:

```bash
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:

```bash
python setup.py build install
```

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


