%global _empty_manifest_terminate_build 0 Name: python-cbgen Version: 1.0.2 Release: 1 Summary: Python wrapper around a BGEN library License: MIT URL: https://github.com/limix/cbgen Source0: https://mirrors.nju.edu.cn/pypi/web/packages/4b/ea/76eb6a4361bb5927ff29a96baf5668296905bdffe90cc31e692728fc3574/cbgen-1.0.2.tar.gz BuildArch: noarch Requires: python3-appdirs Requires: python3-build Requires: python3-cffi Requires: python3-numpy Requires: python3-pooch Requires: python3-pytest Requires: python3-toml %description # cbgen Python wrapper around a BGEN library. ([cbgen documentation](https://cbgen.readthedocs.io)). [BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) is a file format for storing large genetic datasets. It supports both unphased genotypes and phased haplotype data with variable ploidy and number of alleles. It was designed to provide a compact data representation without sacrificing variant access performance. This Python package is a wrapper around the [bgen library](https://github.com/limix/bgen), a low-memory footprint reader that efficiently reads bgen files. It fully supports the bgen format specifications: 1.2 and 1.3; as well as their optional compressed formats. ## Installation ```bash pip install cbgen ``` ## Usage example ```python >>> import cbgen >>> >>> bgen = cbgen.bgen_file(cbgen.example.get("haplotypes.bgen")) >>> bgen.create_metafile("haplotypes.bgen.metafile") >>> mf = cbgen.bgen_metafile("haplotypes.bgen.metafile") >>> print(mf.npartitions) 1 >>> print(mf.nvariants) 4 >>> print(mf.partition_size) 4 >>> part = mf.read_partition(0) >>> gt = bgen.read_genotype(part.variants.offset[0]) >>> print(gt.probability) [[1. 0. 1. 0.] [0. 1. 1. 0.] [1. 0. 0. 1.] [0. 1. 0. 1.]] >>> mf.close() >>> bgen.close() ``` ## Authors * [Carl Kadie](https://github.com/CarlKCarlK) * [Danilo Horta](https://github.com/horta) ## License This project is licensed under the [MIT License](https://raw.githubusercontent.com/limix/cbgen/main/LICENSE). %package -n python3-cbgen Summary: Python wrapper around a BGEN library Provides: python-cbgen BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-cbgen # cbgen Python wrapper around a BGEN library. ([cbgen documentation](https://cbgen.readthedocs.io)). [BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) is a file format for storing large genetic datasets. It supports both unphased genotypes and phased haplotype data with variable ploidy and number of alleles. It was designed to provide a compact data representation without sacrificing variant access performance. This Python package is a wrapper around the [bgen library](https://github.com/limix/bgen), a low-memory footprint reader that efficiently reads bgen files. It fully supports the bgen format specifications: 1.2 and 1.3; as well as their optional compressed formats. ## Installation ```bash pip install cbgen ``` ## Usage example ```python >>> import cbgen >>> >>> bgen = cbgen.bgen_file(cbgen.example.get("haplotypes.bgen")) >>> bgen.create_metafile("haplotypes.bgen.metafile") >>> mf = cbgen.bgen_metafile("haplotypes.bgen.metafile") >>> print(mf.npartitions) 1 >>> print(mf.nvariants) 4 >>> print(mf.partition_size) 4 >>> part = mf.read_partition(0) >>> gt = bgen.read_genotype(part.variants.offset[0]) >>> print(gt.probability) [[1. 0. 1. 0.] [0. 1. 1. 0.] [1. 0. 0. 1.] [0. 1. 0. 1.]] >>> mf.close() >>> bgen.close() ``` ## Authors * [Carl Kadie](https://github.com/CarlKCarlK) * [Danilo Horta](https://github.com/horta) ## License This project is licensed under the [MIT License](https://raw.githubusercontent.com/limix/cbgen/main/LICENSE). %package help Summary: Development documents and examples for cbgen Provides: python3-cbgen-doc %description help # cbgen Python wrapper around a BGEN library. ([cbgen documentation](https://cbgen.readthedocs.io)). [BGEN](https://www.well.ox.ac.uk/~gav/bgen_format/) is a file format for storing large genetic datasets. It supports both unphased genotypes and phased haplotype data with variable ploidy and number of alleles. It was designed to provide a compact data representation without sacrificing variant access performance. This Python package is a wrapper around the [bgen library](https://github.com/limix/bgen), a low-memory footprint reader that efficiently reads bgen files. It fully supports the bgen format specifications: 1.2 and 1.3; as well as their optional compressed formats. ## Installation ```bash pip install cbgen ``` ## Usage example ```python >>> import cbgen >>> >>> bgen = cbgen.bgen_file(cbgen.example.get("haplotypes.bgen")) >>> bgen.create_metafile("haplotypes.bgen.metafile") >>> mf = cbgen.bgen_metafile("haplotypes.bgen.metafile") >>> print(mf.npartitions) 1 >>> print(mf.nvariants) 4 >>> print(mf.partition_size) 4 >>> part = mf.read_partition(0) >>> gt = bgen.read_genotype(part.variants.offset[0]) >>> print(gt.probability) [[1. 0. 1. 0.] [0. 1. 1. 0.] [1. 0. 0. 1.] [0. 1. 0. 1.]] >>> mf.close() >>> bgen.close() ``` ## Authors * [Carl Kadie](https://github.com/CarlKCarlK) * [Danilo Horta](https://github.com/horta) ## License This project is licensed under the [MIT License](https://raw.githubusercontent.com/limix/cbgen/main/LICENSE). %prep %autosetup -n cbgen-1.0.2 %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-cbgen -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Fri May 05 2023 Python_Bot - 1.0.2-1 - Package Spec generated