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| author | CoprDistGit <infra@openeuler.org> | 2023-05-05 13:21:10 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-05 13:21:10 +0000 |
| commit | 1fa25066f2c3c3c0f63f2876dc7fd45c2a42089f (patch) | |
| tree | 2c669cb73950fbf4e2b00ee295261ce25984c37f | |
| parent | 91aedc82be629f8d5b5abba018e5c2e489d021ea (diff) | |
automatic import of python-cbgenopeneuler20.03
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-cbgen.spec | 241 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 243 insertions, 0 deletions
@@ -0,0 +1 @@ +/cbgen-1.0.2.tar.gz diff --git a/python-cbgen.spec b/python-cbgen.spec new file mode 100644 index 0000000..13038a5 --- /dev/null +++ b/python-cbgen.spec @@ -0,0 +1,241 @@ +%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 <Python_Bot@openeuler.org> - 1.0.2-1 +- Package Spec generated @@ -0,0 +1 @@ +8c762476f6a836b3bf1d3f3fad23d9d4 cbgen-1.0.2.tar.gz |
