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|
%global _empty_manifest_terminate_build 0
Name: python-cooler
Version: 0.9.2
Release: 1
Summary: Sparse binary format for genomic interaction matrices.
License: BSD-3-Clause
URL: https://pypi.org/project/cooler/
Source0: https://mirrors.aliyun.com/pypi/web/packages/cc/ee/455b5cd4f9056eefaefb07b0ec5e1c9681c84756f4eaf585009e234d20f4/cooler-0.9.2.tar.gz
BuildArch: noarch
Requires: python3-Sphinx
Requires: python3-sphinx-rtd-theme
Requires: python3-numpy
Requires: python3-scipy
Requires: python3-pandas
Requires: python3-h5py
Requires: python3-click
Requires: python3-cytoolz
Requires: python3-multiprocess
Requires: python3-pyfaidx
Requires: python3-asciitree
Requires: python3-pyyaml
Requires: python3-simplejson
Requires: python3-biopython
Requires: python3-dask[array,dataframe]
Requires: python3-ipytree
Requires: python3-ipywidgets
Requires: python3-matplotlib
Requires: python3-pypairix
Requires: python3-psutil
Requires: python3-pysam
Requires: python3-m2r
Requires: python3-numpydoc
Requires: python3-recommonmark
Requires: python3-coverage[toml]
Requires: python3-flake8
Requires: python3-flake8-pyproject
Requires: python3-isort
Requires: python3-pytest
Requires: python3-pytest-cov
%description
# Cooler
<a href="https://open2c.github.io/cooler"><img width="25%" src="https://github.com/open2c/cooler/raw/master/docs/cooler_logo.png" alt="Cooler"></a>
<table>
<tr>
<td>Latest Release</td>
<td>
<a href="https://pypi.org/project/cooler/">
<img src="https://img.shields.io/pypi/v/cooler?color=blue&label=PyPI%20package" alt="latest release pypi">
</a>
<a href="https://bioconda.github.io/recipes/cooler/README.html">
<img src="https://img.shields.io/conda/vn/bioconda/cooler?color=blue" alt="latest release bioconda">
</a>
</td>
</tr>
<tr>
<td>License</td>
<td>
<a href="https://github.com/open2c/cooler/blob/master/LICENSE">
<img src="https://img.shields.io/badge/license-BSD-green" alt="license">
<!-- <img src="https://img.shields.io/pypi/l/cooler.svg" alt="license"> -->
</a>
</td>
</tr>
<tr>
<td>Build Status</td>
<td>
<a href="https://github.com/open2c/cooler/blob/master/.github/workflows/ci.yml">
<img src="https://github.com/open2c/cooler/actions/workflows/ci.yml/badge.svg" alt="build status">
</a>
</td>
</tr>
<tr>
<td>Pre-commit Status</td>
<td>
<a href="https://results.pre-commit.ci/repo/github/49553222">
<img src="https://results.pre-commit.ci/badge/github/open2c/cooler/master.svg" alt="pre-commit status" />
</a>
</td>
</tr>
<tr>
<td>Docs Status</td>
<td>
<a href="http://cooler.readthedocs.org/en/latest/">
<img src="https://readthedocs.org/projects/cooler/badge/?version=latest">
</a>
</td>
</tr>
<tr>
<td>Coverage</td>
<td>
<a href="https://codecov.io/gh/open2c/cooler">
<img src="https://codecov.io/gh/open2c/cooler/branch/master/graph/badge.svg" alt="coverage">
</a>
</td>
</tr>
<tr>
<td>Downloads</td>
<td>
<a href="https://pypi.org/project/cooler">
<img src="https://static.pepy.tech/personalized-badge/cooler?period=total&units=international_system&left_color=grey&right_color=blue&left_text=PyPI%20downloads" alt="pypi downloads">
</a>
<a href="http://bioconda.github.io/recipes/cooler/README.html">
<img src="https://img.shields.io/conda/dn/bioconda/cooler.svg?style=flat&label=Bioconda downloads" alt="bioconda downloads">
</a>
</td>
</tr>
<tr>
<td>Citation</td>
<td>
<a href="https://doi.org/10.1093/bioinformatics/btz540">
<img src="https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtz540-blue" alt="paper doi">
</a>
<a href="https://zenodo.org/badge/latestdoi/49553222">
<img src="https://zenodo.org/badge/49553222.svg" alt="zenodo doi">
</a>
</td>
</tr>
<tr>
<td>Community</td>
<td>
<a href="https://bit.ly/open2c-slack">
<img src="https://img.shields.io/badge/chat-slack-%233F0F3F?logo=slack" alt="slack">
</a>
</td>
</tr>
</table>
## A cool place to store your Hi-C
Cooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
The cooler file format is an implementation of a genomic matrix data model using [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files.
To get started:
- [Install](#Installation) cooler
- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder).
- _cool_ files from published Hi-C data sets are available at `ftp://cooler.csail.mit.edu/coolers`.
- Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index).
### Installation
Install from PyPI using pip.
```sh
$ pip install cooler
```
If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel.
```sh
$ conda install -c conda-forge -c bioconda cooler
```
### Citing
Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. _Bioinformatics_. doi: [10.1093/bioinformatics/btz540](https://doi.org/10.1093/bioinformatics/btz540).
```bibtex
@article{cooler2020,
author = {Abdennur, Nezar and Mirny, Leonid A},
title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}",
journal={Bioinformatics},
volume={36},
number={1},
pages={311--316},
year={2020},
doi = {10.1093/bioinformatics/btz540},
url = {https://doi.org/10.1093/bioinformatics/btz540},
}
```
### Contributing
Interested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md).
### Related projects
- Process Hi-C data with [distiller](https://github.com/open2c/distiller)!
- Downstream analysis with [cooltools](https://github.com/open2c/cooltools)!
- Visualize your cooler data with [HiGlass](http://higlass.io)!
%package -n python3-cooler
Summary: Sparse binary format for genomic interaction matrices.
Provides: python-cooler
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-cooler
# Cooler
<a href="https://open2c.github.io/cooler"><img width="25%" src="https://github.com/open2c/cooler/raw/master/docs/cooler_logo.png" alt="Cooler"></a>
<table>
<tr>
<td>Latest Release</td>
<td>
<a href="https://pypi.org/project/cooler/">
<img src="https://img.shields.io/pypi/v/cooler?color=blue&label=PyPI%20package" alt="latest release pypi">
</a>
<a href="https://bioconda.github.io/recipes/cooler/README.html">
<img src="https://img.shields.io/conda/vn/bioconda/cooler?color=blue" alt="latest release bioconda">
</a>
</td>
</tr>
<tr>
<td>License</td>
<td>
<a href="https://github.com/open2c/cooler/blob/master/LICENSE">
<img src="https://img.shields.io/badge/license-BSD-green" alt="license">
<!-- <img src="https://img.shields.io/pypi/l/cooler.svg" alt="license"> -->
</a>
</td>
</tr>
<tr>
<td>Build Status</td>
<td>
<a href="https://github.com/open2c/cooler/blob/master/.github/workflows/ci.yml">
<img src="https://github.com/open2c/cooler/actions/workflows/ci.yml/badge.svg" alt="build status">
</a>
</td>
</tr>
<tr>
<td>Pre-commit Status</td>
<td>
<a href="https://results.pre-commit.ci/repo/github/49553222">
<img src="https://results.pre-commit.ci/badge/github/open2c/cooler/master.svg" alt="pre-commit status" />
</a>
</td>
</tr>
<tr>
<td>Docs Status</td>
<td>
<a href="http://cooler.readthedocs.org/en/latest/">
<img src="https://readthedocs.org/projects/cooler/badge/?version=latest">
</a>
</td>
</tr>
<tr>
<td>Coverage</td>
<td>
<a href="https://codecov.io/gh/open2c/cooler">
<img src="https://codecov.io/gh/open2c/cooler/branch/master/graph/badge.svg" alt="coverage">
</a>
</td>
</tr>
<tr>
<td>Downloads</td>
<td>
<a href="https://pypi.org/project/cooler">
<img src="https://static.pepy.tech/personalized-badge/cooler?period=total&units=international_system&left_color=grey&right_color=blue&left_text=PyPI%20downloads" alt="pypi downloads">
</a>
<a href="http://bioconda.github.io/recipes/cooler/README.html">
<img src="https://img.shields.io/conda/dn/bioconda/cooler.svg?style=flat&label=Bioconda downloads" alt="bioconda downloads">
</a>
</td>
</tr>
<tr>
<td>Citation</td>
<td>
<a href="https://doi.org/10.1093/bioinformatics/btz540">
<img src="https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtz540-blue" alt="paper doi">
</a>
<a href="https://zenodo.org/badge/latestdoi/49553222">
<img src="https://zenodo.org/badge/49553222.svg" alt="zenodo doi">
</a>
</td>
</tr>
<tr>
<td>Community</td>
<td>
<a href="https://bit.ly/open2c-slack">
<img src="https://img.shields.io/badge/chat-slack-%233F0F3F?logo=slack" alt="slack">
</a>
</td>
</tr>
</table>
## A cool place to store your Hi-C
Cooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
The cooler file format is an implementation of a genomic matrix data model using [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files.
To get started:
- [Install](#Installation) cooler
- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder).
- _cool_ files from published Hi-C data sets are available at `ftp://cooler.csail.mit.edu/coolers`.
- Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index).
### Installation
Install from PyPI using pip.
```sh
$ pip install cooler
```
If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel.
```sh
$ conda install -c conda-forge -c bioconda cooler
```
### Citing
Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. _Bioinformatics_. doi: [10.1093/bioinformatics/btz540](https://doi.org/10.1093/bioinformatics/btz540).
```bibtex
@article{cooler2020,
author = {Abdennur, Nezar and Mirny, Leonid A},
title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}",
journal={Bioinformatics},
volume={36},
number={1},
pages={311--316},
year={2020},
doi = {10.1093/bioinformatics/btz540},
url = {https://doi.org/10.1093/bioinformatics/btz540},
}
```
### Contributing
Interested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md).
### Related projects
- Process Hi-C data with [distiller](https://github.com/open2c/distiller)!
- Downstream analysis with [cooltools](https://github.com/open2c/cooltools)!
- Visualize your cooler data with [HiGlass](http://higlass.io)!
%package help
Summary: Development documents and examples for cooler
Provides: python3-cooler-doc
%description help
# Cooler
<a href="https://open2c.github.io/cooler"><img width="25%" src="https://github.com/open2c/cooler/raw/master/docs/cooler_logo.png" alt="Cooler"></a>
<table>
<tr>
<td>Latest Release</td>
<td>
<a href="https://pypi.org/project/cooler/">
<img src="https://img.shields.io/pypi/v/cooler?color=blue&label=PyPI%20package" alt="latest release pypi">
</a>
<a href="https://bioconda.github.io/recipes/cooler/README.html">
<img src="https://img.shields.io/conda/vn/bioconda/cooler?color=blue" alt="latest release bioconda">
</a>
</td>
</tr>
<tr>
<td>License</td>
<td>
<a href="https://github.com/open2c/cooler/blob/master/LICENSE">
<img src="https://img.shields.io/badge/license-BSD-green" alt="license">
<!-- <img src="https://img.shields.io/pypi/l/cooler.svg" alt="license"> -->
</a>
</td>
</tr>
<tr>
<td>Build Status</td>
<td>
<a href="https://github.com/open2c/cooler/blob/master/.github/workflows/ci.yml">
<img src="https://github.com/open2c/cooler/actions/workflows/ci.yml/badge.svg" alt="build status">
</a>
</td>
</tr>
<tr>
<td>Pre-commit Status</td>
<td>
<a href="https://results.pre-commit.ci/repo/github/49553222">
<img src="https://results.pre-commit.ci/badge/github/open2c/cooler/master.svg" alt="pre-commit status" />
</a>
</td>
</tr>
<tr>
<td>Docs Status</td>
<td>
<a href="http://cooler.readthedocs.org/en/latest/">
<img src="https://readthedocs.org/projects/cooler/badge/?version=latest">
</a>
</td>
</tr>
<tr>
<td>Coverage</td>
<td>
<a href="https://codecov.io/gh/open2c/cooler">
<img src="https://codecov.io/gh/open2c/cooler/branch/master/graph/badge.svg" alt="coverage">
</a>
</td>
</tr>
<tr>
<td>Downloads</td>
<td>
<a href="https://pypi.org/project/cooler">
<img src="https://static.pepy.tech/personalized-badge/cooler?period=total&units=international_system&left_color=grey&right_color=blue&left_text=PyPI%20downloads" alt="pypi downloads">
</a>
<a href="http://bioconda.github.io/recipes/cooler/README.html">
<img src="https://img.shields.io/conda/dn/bioconda/cooler.svg?style=flat&label=Bioconda downloads" alt="bioconda downloads">
</a>
</td>
</tr>
<tr>
<td>Citation</td>
<td>
<a href="https://doi.org/10.1093/bioinformatics/btz540">
<img src="https://img.shields.io/badge/DOI-10.1093%2Fbioinformatics%2Fbtz540-blue" alt="paper doi">
</a>
<a href="https://zenodo.org/badge/latestdoi/49553222">
<img src="https://zenodo.org/badge/49553222.svg" alt="zenodo doi">
</a>
</td>
</tr>
<tr>
<td>Community</td>
<td>
<a href="https://bit.ly/open2c-slack">
<img src="https://img.shields.io/badge/chat-slack-%233F0F3F?logo=slack" alt="slack">
</a>
</td>
</tr>
</table>
## A cool place to store your Hi-C
Cooler is a support library for a **sparse, compressed, binary** persistent storage [format](http://cooler.readthedocs.io/en/latest/schema.html), also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
The cooler file format is an implementation of a genomic matrix data model using [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) as the container format. The `cooler` package includes a suite of [command line tools](http://cooler.readthedocs.io/en/latest/cli.html) and a [Python API](http://cooler.readthedocs.io/en/latest/api.html) to facilitate creating, querying and manipulating cooler files.
To get started:
- [Install](#Installation) cooler
- Read the [documentation](http://cooler.readthedocs.org/en/stable/) and see the Jupyter Notebook [walkthrough](https://github.com/open2c/cooler-binder).
- _cool_ files from published Hi-C data sets are available at `ftp://cooler.csail.mit.edu/coolers`.
- Many more multires (_mcool_) files are available on the [4DN data portal](https://data.4dnucleome.org/visualization/index).
### Installation
Install from PyPI using pip.
```sh
$ pip install cooler
```
If you are using `conda`, you can alternatively install `cooler` from the [bioconda](https://bioconda.github.io/index.html) channel.
```sh
$ conda install -c conda-forge -c bioconda cooler
```
### Citing
Abdennur, N., and Mirny, L.A. (2020). Cooler: scalable storage for Hi-C data and other genomically labeled arrays. _Bioinformatics_. doi: [10.1093/bioinformatics/btz540](https://doi.org/10.1093/bioinformatics/btz540).
```bibtex
@article{cooler2020,
author = {Abdennur, Nezar and Mirny, Leonid A},
title = "{Cooler: scalable storage for Hi-C data and other genomically labeled arrays}",
journal={Bioinformatics},
volume={36},
number={1},
pages={311--316},
year={2020},
doi = {10.1093/bioinformatics/btz540},
url = {https://doi.org/10.1093/bioinformatics/btz540},
}
```
### Contributing
Interested in contributing to cooler? That's great! To get started, check out the [contributing guide](https://github.com/open2c/cooler/blob/master/CONTRIBUTING.md).
### Related projects
- Process Hi-C data with [distiller](https://github.com/open2c/distiller)!
- Downstream analysis with [cooltools](https://github.com/open2c/cooltools)!
- Visualize your cooler data with [HiGlass](http://higlass.io)!
%prep
%autosetup -n cooler-0.9.2
%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-cooler -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Thu Jun 08 2023 Python_Bot <Python_Bot@openeuler.org> - 0.9.2-1
- Package Spec generated
|
