%global _empty_manifest_terminate_build 0 Name: python-HTSeq Version: 2.0.2 Release: 1 Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays License: GPL3 URL: https://github.com/htseq Source0: https://mirrors.nju.edu.cn/pypi/web/packages/de/13/cbeb753eb29d31bb252bc18443e79a3739bf5bd3dbc99e65fcf13db81be1/HTSeq-2.0.2.tar.gz BuildArch: noarch Requires: python3-numpy Requires: python3-pysam Requires: python3-matplotlib Requires: python3-scipy Requires: python3-pytest Requires: python3-pandas Requires: python3-matplotlib %description ![CI](https://github.com/htseq/htseq/workflows/CI/badge.svg) [![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 **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 %package -n python3-HTSeq Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays Provides: python-HTSeq BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-HTSeq ![CI](https://github.com/htseq/htseq/workflows/CI/badge.svg) [![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 **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 %package help Summary: Development documents and examples for HTSeq Provides: python3-HTSeq-doc %description help ![CI](https://github.com/htseq/htseq/workflows/CI/badge.svg) [![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 **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 %prep %autosetup -n HTSeq-2.0.2 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-HTSeq -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Tue Apr 25 2023 Python_Bot - 2.0.2-1 - Package Spec generated