HTSeq 2.0.7__cp312-cp312-macosx_10_9_x86_64.whl

HTSeq-2.0.7.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: HTSeq
+Version: 2.0.7
+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
+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
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pysam
+Provides-Extra: htseq-qa
+Requires-Dist: matplotlib >=1.4 ; extra == 'htseq-qa'
+Provides-Extra: test
+Requires-Dist: scipy >=1.5.0 ; extra == 'test'
+Requires-Dist: pytest >=6.2.5 ; extra == 'test'
+Requires-Dist: pandas >=1.1.0 ; extra == 'test'
+Requires-Dist: matplotlib >=1.4 ; extra == 'test'
+
+![CI](https://github.com/htseq/htseq/actions/workflows/ci.yml/badge.svg?branch=main)
+[![Documentation Status](https://readthedocs.org/projects/htseq/badge/?version=latest)](https://htseq.readthedocs.io)
+
+# HTSeq
+**DEVS**: https://github.com/htseq/htseq
+
+**DOCS**: https://htseq.readthedocs.io
+
+**CITATION** (please cite this new paper!): Putri et al. Analysing high-throughput sequencing data in Python with HTSeq 2.0. Bioinformatics, btac166, [https://doi.org/10.1093/bioinformatics/btac166](https://doi.org/10.1093/bioinformatics/btac166) (2022).
+
+A Python library to facilitate programmatic analysis of data
+from high-throughput sequencing (HTS) experiments. A popular component of ``HTSeq``
+is ``htseq-count``, a script to quantify gene expression in bulk and single-cell RNA-Seq
+and similar experiments.
+
+## Requirements
+
+To use ``HTSeq`` you need:
+
+-  ``Python >= 3.7`` (**note**: ``Python 2.7`` support has been dropped)
+-  ``numpy``
+-  ``pysam``
+
+To manipulate BigWig files, you also need:
+
+- ``pyBigWig``
+
+To run the ``htseq-qa`` script, you also need:
+
+-  ``matplotlib``
+
+To run ``htseq-count`` and ``htseq-count-barcodes`` with custom output formats for the counts table, you need:
+
+- ``mtx`` file: ``scipy``
+- ``h5ad`` file: ``anndata``
+- ``loom`` file: ``loompy``
+
+Both **Linux** and **OSX** are supported and binaries are provided on Pypi. We
+would like to support **Windows** but currently lack the expertise to do so. If
+you would like to take on the Windows release and maintenance, please open an
+issue and we'll try to help.
+
+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``
+
+## Installation
+
+### PIP
+
+To install directly from PyPI:
+
+```bash
+pip install HTSeq
+```
+
+To install a specific version:
+
+```bash
+pip install 'HTSeq==2.0.0'
+```
+
+If this fails, please install all dependencies first:
+
+```bash
+pip install matplotlib
+pip install Cython
+pip install pysam
+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
+```
+
+## Testing
+To test locally, run
+
+```bash
+./test.sh
+```
+
+To test `htseq-count` alone, run it with the `-o` option.
+
+A virtual environment is created in the `.venv` folder and `HTSeq` is installed inside it, including all modules and scripts.
+
+## Authors
+- 2021-: Givanna Putri ([ghar1821](https://github.com/ghar1821))
+- 2016-: Fabio Zanini ([iosonofabio](https://github.com/iosonofabio))@ https://fabilab.org
+- 2010-2015: Simon Anders ([simon-anders](https://github.com/simon-anders)), Wolfgang Huber

HTSeq-2.0.7.dist-info/RECORD

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HTSeq-2.0.7.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: bdist_wheel (0.43.0)
+Root-Is-Purelib: false
+Tag: cp312-cp312-macosx_10_9_x86_64
+

HTSeq-2.0.7.dist-info/top_level.txt

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+HTSeq