From c52b9e487ef72bcf709c35bf6fe616b27c279014 Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Tue, 11 Apr 2023 10:26:57 +0000 Subject: automatic import of python-bx-python --- .gitignore | 1 + python-bx-python.spec | 178 ++++++++++++++++++++++++++++++++++++++++++++++++++ sources | 1 + 3 files changed, 180 insertions(+) create mode 100644 python-bx-python.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore index e69de29..ef2f003 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1 @@ +/bx-python-0.9.0.tar.gz diff --git a/python-bx-python.spec b/python-bx-python.spec new file mode 100644 index 0000000..03d5f9f --- /dev/null +++ b/python-bx-python.spec @@ -0,0 +1,178 @@ +%global _empty_manifest_terminate_build 0 +Name: python-bx-python +Version: 0.9.0 +Release: 1 +Summary: Tools for manipulating biological data, particularly multiple sequence alignments +License: MIT +URL: https://github.com/bxlab/bx-python +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/b1/79/6159768ef08fc5d037c184bc964d7a79984ac99d0c076b70251c89964550/bx-python-0.9.0.tar.gz +BuildArch: noarch + +Requires: python3-numpy + +%description +[![Build Status](https://travis-ci.org/bxlab/bx-python.svg?branch=master)](https://travis-ci.org/bxlab/bx-python) + +[![Read the Docs](https://img.shields.io/readthedocs/bx-python.svg)](https://bx-python.readthedocs.io/) + +# bx-python + +The bx-python project is a Python library and associated set of scripts for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: + + * Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats) + * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems) + * Data structures for working with intervals on sequences + * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly + * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation + +## Requirements + +Build currently requires liblzo, e.g. sudo apt-get install liblzo2-dev on debian/ubuntu). + +## Installing + +The package can be installed with pip: + +```pip install bx-python``` + +It is available in [bioconda](https://anaconda.org/bioconda/bx-python) (recommended): + +```conda install -c conda-forge -c bioconda bx-python``` + +It is available in [Debian](https://tracker.debian.org/pkg/python-bx) and [Ubuntu](https://packages.ubuntu.com/python3-bx): + +```sudo apt install python3-bx``` + +Or can be built from a checkout of the repository: + +```python setup.py install``` + + +%package -n python3-bx-python +Summary: Tools for manipulating biological data, particularly multiple sequence alignments +Provides: python-bx-python +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-bx-python +[![Build Status](https://travis-ci.org/bxlab/bx-python.svg?branch=master)](https://travis-ci.org/bxlab/bx-python) + +[![Read the Docs](https://img.shields.io/readthedocs/bx-python.svg)](https://bx-python.readthedocs.io/) + +# bx-python + +The bx-python project is a Python library and associated set of scripts for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: + + * Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats) + * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems) + * Data structures for working with intervals on sequences + * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly + * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation + +## Requirements + +Build currently requires liblzo, e.g. sudo apt-get install liblzo2-dev on debian/ubuntu). + +## Installing + +The package can be installed with pip: + +```pip install bx-python``` + +It is available in [bioconda](https://anaconda.org/bioconda/bx-python) (recommended): + +```conda install -c conda-forge -c bioconda bx-python``` + +It is available in [Debian](https://tracker.debian.org/pkg/python-bx) and [Ubuntu](https://packages.ubuntu.com/python3-bx): + +```sudo apt install python3-bx``` + +Or can be built from a checkout of the repository: + +```python setup.py install``` + + +%package help +Summary: Development documents and examples for bx-python +Provides: python3-bx-python-doc +%description help +[![Build Status](https://travis-ci.org/bxlab/bx-python.svg?branch=master)](https://travis-ci.org/bxlab/bx-python) + +[![Read the Docs](https://img.shields.io/readthedocs/bx-python.svg)](https://bx-python.readthedocs.io/) + +# bx-python + +The bx-python project is a Python library and associated set of scripts for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: + + * Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats) + * Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optimized for use over network filesystems) + * Data structures for working with intervals on sequences + * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly + * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation + +## Requirements + +Build currently requires liblzo, e.g. sudo apt-get install liblzo2-dev on debian/ubuntu). + +## Installing + +The package can be installed with pip: + +```pip install bx-python``` + +It is available in [bioconda](https://anaconda.org/bioconda/bx-python) (recommended): + +```conda install -c conda-forge -c bioconda bx-python``` + +It is available in [Debian](https://tracker.debian.org/pkg/python-bx) and [Ubuntu](https://packages.ubuntu.com/python3-bx): + +```sudo apt install python3-bx``` + +Or can be built from a checkout of the repository: + +```python setup.py install``` + + +%prep +%autosetup -n bx-python-0.9.0 + +%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-bx-python -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Tue Apr 11 2023 Python_Bot - 0.9.0-1 +- Package Spec generated diff --git a/sources b/sources new file mode 100644 index 0000000..3b6e601 --- /dev/null +++ b/sources @@ -0,0 +1 @@ +62e6ec6fcd488e4d6b4485ecaac35040 bx-python-0.9.0.tar.gz -- cgit v1.2.3