%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