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diff --git a/python-panchip.spec b/python-panchip.spec new file mode 100644 index 0000000..d9d2fe1 --- /dev/null +++ b/python-panchip.spec @@ -0,0 +1,399 @@ +%global _empty_manifest_terminate_build 0 +Name: python-PanChIP +Version: 3.0.10 +Release: 1 +Summary: Pan-ChIP-seq Analysis of Peak Sets +License: MIT +URL: https://github.com/hanjunlee21/PanChIP +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/2c/4b/e0d311250d07ab0323c38ab2bda21cdb22dff7ba99054b45cb2e236b4182/PanChIP-3.0.10.tar.gz +BuildArch: noarch + + +%description +# PanChIP + +[](https://badge.fury.io/py/PanChIP) + +**Pan-ChIP-seq Analysis of Protein Colocalization Using Peak Sets** + +The current version of PanChIP supports the hg38 genome assembly. + +## Prerequisites +Python 3, BEDTools + +## Installation +```shell +pip3 install panchip +``` + +## Input +```shell +PanChIP Analysis: a directory with only 6-column BED files +PanChIP Filter: a 6-column BED file + +We recommend most PanChIP users to utilize BED files with constant non-zero fifth column values (e.g., 1, 500, 1000). +``` + +## Usage + +### panchip <command> [options] + +```shell +Commands: + init Initialization of the PanChIP library + analysis Analysis of a list peak sets + filter Filtering library for quality control +Run panchip <command> -h for help on a specific command. + +PanChIP: Pan-ChIP-seq Analysis of Peak Sets + +positional arguments: + command Subcommand to run + +optional arguments: + -h, --help show this help message and exit + --version show program's version number and exit +``` + +### panchip init [-h] library_directory + +```shell + +Initialization of the PanChIP library + +positional arguments: + library_directory Directory wherein PanChIP library will be stored. > 13.6 + GB of storage required. + +optional arguments: + -h, --help show this help message and exit +``` + +### panchip analysis [-h] [-t THREADS] [-r REPEATS] library_directory input_directory output_directory + +```shell + +Analysis of a list peak sets + +positional arguments: + library_directory Directory wherein PanChIP library was stored. + input_directory Input directory wherein peak sets in the format of .bed + files are located. + (.bed6 format with numeric scores in 5th column required) + output_directory Output directory wherein output files will be stored. + +optional arguments: + -h, --help show this help message and exit + -t THREADS Number of threads to use. (default: 1) + -r REPEATS Number of repeats to perform. (default: 1) +``` + +### panchip filter [-h] [-t THREADS] library_directory input_file output_directory + +```shell + +Filtering library for quality control + +positional arguments: + library_directory Directory wherein PanChIP library was stored. + input_file Path to the input .bed file. + (.bed6 format with numeric scores in 5th column required) + output_directory Output directory wherein output files will be stored. + +optional arguments: + -h, --help show this help message and exit + -t THREADS Number of threads to use. (default: 1) +``` + +## Primary Citation + +Please cite the original PanChIP paper for works that utilized the PanChIP software. + +- **Sanidas I, Lee H, Rumde PH, Boulay G, Morris R, Golczer G, Stanzione M, Hajizadeh S, Zhong J, Ryan MB, Corcoran RB, Drapkin BJ, Rivera MN, Dyson NJ, and Lawrence MS. Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci, and is redistributed by cell cycle progression. _Forthcoming_.** + +## Extended Citation + +The development of PanChIP was possible thanks to many groundbreaking works of fellow researchers. We highly recommend users to cite the Cistrome Data Browser as well. + +- **Zheng R, Wan C, Mei S, Qin Q, Wu Q, Sun H, Chen C-H, Brown M, Zhang X, Meyer CA, and Liu XS. Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. _Nucleic Acids Research_ 47.D1, D729–D735 (2019).** + +While the design of PanChIP is different from that of BART, we suggest users to also try out the BART software. PanChIP measures the overlap between peak sets, while BART assesses the predictability of profiles based on the library. + +- **Wang Z, Civelek M, Miller CL, Sheffield NC, Guertin MJ, and Zang C. BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. _Bioinformatics_ 34.16, 2867–2869 (2018).** + +%package -n python3-PanChIP +Summary: Pan-ChIP-seq Analysis of Peak Sets +Provides: python-PanChIP +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-PanChIP +# PanChIP + +[](https://badge.fury.io/py/PanChIP) + +**Pan-ChIP-seq Analysis of Protein Colocalization Using Peak Sets** + +The current version of PanChIP supports the hg38 genome assembly. + +## Prerequisites +Python 3, BEDTools + +## Installation +```shell +pip3 install panchip +``` + +## Input +```shell +PanChIP Analysis: a directory with only 6-column BED files +PanChIP Filter: a 6-column BED file + +We recommend most PanChIP users to utilize BED files with constant non-zero fifth column values (e.g., 1, 500, 1000). +``` + +## Usage + +### panchip <command> [options] + +```shell +Commands: + init Initialization of the PanChIP library + analysis Analysis of a list peak sets + filter Filtering library for quality control +Run panchip <command> -h for help on a specific command. + +PanChIP: Pan-ChIP-seq Analysis of Peak Sets + +positional arguments: + command Subcommand to run + +optional arguments: + -h, --help show this help message and exit + --version show program's version number and exit +``` + +### panchip init [-h] library_directory + +```shell + +Initialization of the PanChIP library + +positional arguments: + library_directory Directory wherein PanChIP library will be stored. > 13.6 + GB of storage required. + +optional arguments: + -h, --help show this help message and exit +``` + +### panchip analysis [-h] [-t THREADS] [-r REPEATS] library_directory input_directory output_directory + +```shell + +Analysis of a list peak sets + +positional arguments: + library_directory Directory wherein PanChIP library was stored. + input_directory Input directory wherein peak sets in the format of .bed + files are located. + (.bed6 format with numeric scores in 5th column required) + output_directory Output directory wherein output files will be stored. + +optional arguments: + -h, --help show this help message and exit + -t THREADS Number of threads to use. (default: 1) + -r REPEATS Number of repeats to perform. (default: 1) +``` + +### panchip filter [-h] [-t THREADS] library_directory input_file output_directory + +```shell + +Filtering library for quality control + +positional arguments: + library_directory Directory wherein PanChIP library was stored. + input_file Path to the input .bed file. + (.bed6 format with numeric scores in 5th column required) + output_directory Output directory wherein output files will be stored. + +optional arguments: + -h, --help show this help message and exit + -t THREADS Number of threads to use. (default: 1) +``` + +## Primary Citation + +Please cite the original PanChIP paper for works that utilized the PanChIP software. + +- **Sanidas I, Lee H, Rumde PH, Boulay G, Morris R, Golczer G, Stanzione M, Hajizadeh S, Zhong J, Ryan MB, Corcoran RB, Drapkin BJ, Rivera MN, Dyson NJ, and Lawrence MS. Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci, and is redistributed by cell cycle progression. _Forthcoming_.** + +## Extended Citation + +The development of PanChIP was possible thanks to many groundbreaking works of fellow researchers. We highly recommend users to cite the Cistrome Data Browser as well. + +- **Zheng R, Wan C, Mei S, Qin Q, Wu Q, Sun H, Chen C-H, Brown M, Zhang X, Meyer CA, and Liu XS. Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. _Nucleic Acids Research_ 47.D1, D729–D735 (2019).** + +While the design of PanChIP is different from that of BART, we suggest users to also try out the BART software. PanChIP measures the overlap between peak sets, while BART assesses the predictability of profiles based on the library. + +- **Wang Z, Civelek M, Miller CL, Sheffield NC, Guertin MJ, and Zang C. BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. _Bioinformatics_ 34.16, 2867–2869 (2018).** + +%package help +Summary: Development documents and examples for PanChIP +Provides: python3-PanChIP-doc +%description help +# PanChIP + +[](https://badge.fury.io/py/PanChIP) + +**Pan-ChIP-seq Analysis of Protein Colocalization Using Peak Sets** + +The current version of PanChIP supports the hg38 genome assembly. + +## Prerequisites +Python 3, BEDTools + +## Installation +```shell +pip3 install panchip +``` + +## Input +```shell +PanChIP Analysis: a directory with only 6-column BED files +PanChIP Filter: a 6-column BED file + +We recommend most PanChIP users to utilize BED files with constant non-zero fifth column values (e.g., 1, 500, 1000). +``` + +## Usage + +### panchip <command> [options] + +```shell +Commands: + init Initialization of the PanChIP library + analysis Analysis of a list peak sets + filter Filtering library for quality control +Run panchip <command> -h for help on a specific command. + +PanChIP: Pan-ChIP-seq Analysis of Peak Sets + +positional arguments: + command Subcommand to run + +optional arguments: + -h, --help show this help message and exit + --version show program's version number and exit +``` + +### panchip init [-h] library_directory + +```shell + +Initialization of the PanChIP library + +positional arguments: + library_directory Directory wherein PanChIP library will be stored. > 13.6 + GB of storage required. + +optional arguments: + -h, --help show this help message and exit +``` + +### panchip analysis [-h] [-t THREADS] [-r REPEATS] library_directory input_directory output_directory + +```shell + +Analysis of a list peak sets + +positional arguments: + library_directory Directory wherein PanChIP library was stored. + input_directory Input directory wherein peak sets in the format of .bed + files are located. + (.bed6 format with numeric scores in 5th column required) + output_directory Output directory wherein output files will be stored. + +optional arguments: + -h, --help show this help message and exit + -t THREADS Number of threads to use. (default: 1) + -r REPEATS Number of repeats to perform. (default: 1) +``` + +### panchip filter [-h] [-t THREADS] library_directory input_file output_directory + +```shell + +Filtering library for quality control + +positional arguments: + library_directory Directory wherein PanChIP library was stored. + input_file Path to the input .bed file. + (.bed6 format with numeric scores in 5th column required) + output_directory Output directory wherein output files will be stored. + +optional arguments: + -h, --help show this help message and exit + -t THREADS Number of threads to use. (default: 1) +``` + +## Primary Citation + +Please cite the original PanChIP paper for works that utilized the PanChIP software. + +- **Sanidas I, Lee H, Rumde PH, Boulay G, Morris R, Golczer G, Stanzione M, Hajizadeh S, Zhong J, Ryan MB, Corcoran RB, Drapkin BJ, Rivera MN, Dyson NJ, and Lawrence MS. Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci, and is redistributed by cell cycle progression. _Forthcoming_.** + +## Extended Citation + +The development of PanChIP was possible thanks to many groundbreaking works of fellow researchers. We highly recommend users to cite the Cistrome Data Browser as well. + +- **Zheng R, Wan C, Mei S, Qin Q, Wu Q, Sun H, Chen C-H, Brown M, Zhang X, Meyer CA, and Liu XS. Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. _Nucleic Acids Research_ 47.D1, D729–D735 (2019).** + +While the design of PanChIP is different from that of BART, we suggest users to also try out the BART software. PanChIP measures the overlap between peak sets, while BART assesses the predictability of profiles based on the library. + +- **Wang Z, Civelek M, Miller CL, Sheffield NC, Guertin MJ, and Zang C. BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. _Bioinformatics_ 34.16, 2867–2869 (2018).** + +%prep +%autosetup -n PanChIP-3.0.10 + +%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-PanChIP -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 3.0.10-1 +- Package Spec generated |