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authorCoprDistGit <infra@openeuler.org>2023-05-05 13:21:10 +0000
committerCoprDistGit <infra@openeuler.org>2023-05-05 13:21:10 +0000
commit1fa25066f2c3c3c0f63f2876dc7fd45c2a42089f (patch)
tree2c669cb73950fbf4e2b00ee295261ce25984c37f
parent91aedc82be629f8d5b5abba018e5c2e489d021ea (diff)
automatic import of python-cbgenopeneuler20.03
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-rw-r--r--python-cbgen.spec241
-rw-r--r--sources1
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+/cbgen-1.0.2.tar.gz
diff --git a/python-cbgen.spec b/python-cbgen.spec
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+%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
diff --git a/sources b/sources
new file mode 100644
index 0000000..d9591aa
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+8c762476f6a836b3bf1d3f3fad23d9d4 cbgen-1.0.2.tar.gz