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@@ -0,0 +1 @@ +/phylopypruner-1.2.6.tar.gz diff --git a/python-phylopypruner.spec b/python-phylopypruner.spec new file mode 100644 index 0000000..2c02c86 --- /dev/null +++ b/python-phylopypruner.spec @@ -0,0 +1,282 @@ +%global _empty_manifest_terminate_build 0 +Name: python-phylopypruner +Version: 1.2.6 +Release: 1 +Summary: tree-based orthology inference +License: GPL 3 +URL: https://gitlab.com/fethalen/phylopypruner +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/9a/ea/14092f6a69ebb086e3275b5cfa58315ef38d8eab8ca45fcb4a6c4536337c/phylopypruner-1.2.6.tar.gz +BuildArch: noarch + +Requires: python3-setuptools +Requires: python3-wheel +Requires: python3-setuptools-scm + +%description +<img src="https://gitlab.com/fethalen/phylopypruner/raw/master/doc/images/ppp_logo.png" alt="ppp_logotype" width="350"/> + +## About + +*Orthologs* are genes that are related through a speciation event, while +*paralogs* are genes that are related through a gene duplication event. +Accurate identification of orthologs is a prerequisite for phylogenomics, since +including genes that diverged because of a gene duplication event for species +tree inference can cause an erroneous inference of speciation nodes, due to +disparencies between individual gene trees and the species tree. Unfortunately, +contaminants present in even a single taxon can cause a tree-based orthology +inference method to erroneuosly infer paralogy and unnecessarily exclude +sequences. + +PhyloPyPruner is a Python package for phylogenetic tree-based orthology +inference, using the species overlap method. It uses trees and alignments +inferred from the output of a graph-based orthology inference approach, such +as [OrthoMCL](https://www.ncbi.nlm.nih.gov/pubmed/12952885), +[OrthoFinder](https://www.ncbi.nlm.nih.gov/pubmed/26243257) or +[HaMStR](https://www.ncbi.nlm.nih.gov/pubmed/19586527), in order to obtain sets +of sequences that are 1:1 orthologous. In addition to algorithms seen in +pre-existing tree-based tools (for example, +[PhyloTreePruner](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825643/), +[UPhO](https://academic.oup.com/mbe/article/33/8/2117/2578877), +[Agalma](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840672/) or +[Phylogenomic Dataset +Reconstruction](https://www.ncbi.nlm.nih.gov/pubmed/25158799)), this package +provides new methods for reducing potential contamination. + + + +**Figure 1.** A rough overview of a tree-based orthology inference approach. + +## Quick installation + +The easiest way to install PhyloPyPruner is by using the package manager for +Python, [pip](https://pypi.org/project/pip/): + +```bash +pip install phylopypruner # install for all users +pip install --user phylopypruner # install for the current user only +``` + +Once installed, the program is located within `$HOME/.local/bin`. Depending on +your OS, you might have to add the directory to your `$PATH` to avoid typing +the entire path. Once in your path, you run the program like this: + +```bash +phylopypruner +``` + +## [Documentation](https://gitlab.com/fethalen/phylopypruner/wikis) + +1. [About PhyloPyPruner](https://gitlab.com/fethalen/phylopypruner/wikis/introduction) +2. [Tutorial](https://gitlab.com/fethalen/phylopypruner/wikis/tutorial#phylopypruner-tutorial) +3. [Installation](https://gitlab.com/fethalen/phylopypruner/wikis/installation) +4. [Input data](https://gitlab.com/fethalen/phylopypruner/wikis/input-data) +5. [Output files](https://gitlab.com/fethalen/phylopypruner/wikis/output-files) +6. [Methods](https://gitlab.com/fethalen/phylopypruner/wikis/methods) +7. [Options](https://gitlab.com/fethalen/phylopypruner/wikis/options) + +## Cite + +Our manuscript is still in preparation, it will be posted here once a preprint +of the article is available. + +© [Kocot Lab](https://www.kocotlab.com/) 2019 + + + + +%package -n python3-phylopypruner +Summary: tree-based orthology inference +Provides: python-phylopypruner +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-phylopypruner +<img src="https://gitlab.com/fethalen/phylopypruner/raw/master/doc/images/ppp_logo.png" alt="ppp_logotype" width="350"/> + +## About + +*Orthologs* are genes that are related through a speciation event, while +*paralogs* are genes that are related through a gene duplication event. +Accurate identification of orthologs is a prerequisite for phylogenomics, since +including genes that diverged because of a gene duplication event for species +tree inference can cause an erroneous inference of speciation nodes, due to +disparencies between individual gene trees and the species tree. Unfortunately, +contaminants present in even a single taxon can cause a tree-based orthology +inference method to erroneuosly infer paralogy and unnecessarily exclude +sequences. + +PhyloPyPruner is a Python package for phylogenetic tree-based orthology +inference, using the species overlap method. It uses trees and alignments +inferred from the output of a graph-based orthology inference approach, such +as [OrthoMCL](https://www.ncbi.nlm.nih.gov/pubmed/12952885), +[OrthoFinder](https://www.ncbi.nlm.nih.gov/pubmed/26243257) or +[HaMStR](https://www.ncbi.nlm.nih.gov/pubmed/19586527), in order to obtain sets +of sequences that are 1:1 orthologous. In addition to algorithms seen in +pre-existing tree-based tools (for example, +[PhyloTreePruner](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825643/), +[UPhO](https://academic.oup.com/mbe/article/33/8/2117/2578877), +[Agalma](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840672/) or +[Phylogenomic Dataset +Reconstruction](https://www.ncbi.nlm.nih.gov/pubmed/25158799)), this package +provides new methods for reducing potential contamination. + + + +**Figure 1.** A rough overview of a tree-based orthology inference approach. + +## Quick installation + +The easiest way to install PhyloPyPruner is by using the package manager for +Python, [pip](https://pypi.org/project/pip/): + +```bash +pip install phylopypruner # install for all users +pip install --user phylopypruner # install for the current user only +``` + +Once installed, the program is located within `$HOME/.local/bin`. Depending on +your OS, you might have to add the directory to your `$PATH` to avoid typing +the entire path. Once in your path, you run the program like this: + +```bash +phylopypruner +``` + +## [Documentation](https://gitlab.com/fethalen/phylopypruner/wikis) + +1. [About PhyloPyPruner](https://gitlab.com/fethalen/phylopypruner/wikis/introduction) +2. [Tutorial](https://gitlab.com/fethalen/phylopypruner/wikis/tutorial#phylopypruner-tutorial) +3. [Installation](https://gitlab.com/fethalen/phylopypruner/wikis/installation) +4. [Input data](https://gitlab.com/fethalen/phylopypruner/wikis/input-data) +5. [Output files](https://gitlab.com/fethalen/phylopypruner/wikis/output-files) +6. [Methods](https://gitlab.com/fethalen/phylopypruner/wikis/methods) +7. [Options](https://gitlab.com/fethalen/phylopypruner/wikis/options) + +## Cite + +Our manuscript is still in preparation, it will be posted here once a preprint +of the article is available. + +© [Kocot Lab](https://www.kocotlab.com/) 2019 + + + + +%package help +Summary: Development documents and examples for phylopypruner +Provides: python3-phylopypruner-doc +%description help +<img src="https://gitlab.com/fethalen/phylopypruner/raw/master/doc/images/ppp_logo.png" alt="ppp_logotype" width="350"/> + +## About + +*Orthologs* are genes that are related through a speciation event, while +*paralogs* are genes that are related through a gene duplication event. +Accurate identification of orthologs is a prerequisite for phylogenomics, since +including genes that diverged because of a gene duplication event for species +tree inference can cause an erroneous inference of speciation nodes, due to +disparencies between individual gene trees and the species tree. Unfortunately, +contaminants present in even a single taxon can cause a tree-based orthology +inference method to erroneuosly infer paralogy and unnecessarily exclude +sequences. + +PhyloPyPruner is a Python package for phylogenetic tree-based orthology +inference, using the species overlap method. It uses trees and alignments +inferred from the output of a graph-based orthology inference approach, such +as [OrthoMCL](https://www.ncbi.nlm.nih.gov/pubmed/12952885), +[OrthoFinder](https://www.ncbi.nlm.nih.gov/pubmed/26243257) or +[HaMStR](https://www.ncbi.nlm.nih.gov/pubmed/19586527), in order to obtain sets +of sequences that are 1:1 orthologous. In addition to algorithms seen in +pre-existing tree-based tools (for example, +[PhyloTreePruner](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825643/), +[UPhO](https://academic.oup.com/mbe/article/33/8/2117/2578877), +[Agalma](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840672/) or +[Phylogenomic Dataset +Reconstruction](https://www.ncbi.nlm.nih.gov/pubmed/25158799)), this package +provides new methods for reducing potential contamination. + + + +**Figure 1.** A rough overview of a tree-based orthology inference approach. + +## Quick installation + +The easiest way to install PhyloPyPruner is by using the package manager for +Python, [pip](https://pypi.org/project/pip/): + +```bash +pip install phylopypruner # install for all users +pip install --user phylopypruner # install for the current user only +``` + +Once installed, the program is located within `$HOME/.local/bin`. Depending on +your OS, you might have to add the directory to your `$PATH` to avoid typing +the entire path. Once in your path, you run the program like this: + +```bash +phylopypruner +``` + +## [Documentation](https://gitlab.com/fethalen/phylopypruner/wikis) + +1. [About PhyloPyPruner](https://gitlab.com/fethalen/phylopypruner/wikis/introduction) +2. [Tutorial](https://gitlab.com/fethalen/phylopypruner/wikis/tutorial#phylopypruner-tutorial) +3. [Installation](https://gitlab.com/fethalen/phylopypruner/wikis/installation) +4. [Input data](https://gitlab.com/fethalen/phylopypruner/wikis/input-data) +5. [Output files](https://gitlab.com/fethalen/phylopypruner/wikis/output-files) +6. [Methods](https://gitlab.com/fethalen/phylopypruner/wikis/methods) +7. [Options](https://gitlab.com/fethalen/phylopypruner/wikis/options) + +## Cite + +Our manuscript is still in preparation, it will be posted here once a preprint +of the article is available. + +© [Kocot Lab](https://www.kocotlab.com/) 2019 + + + + +%prep +%autosetup -n phylopypruner-1.2.6 + +%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-phylopypruner -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 1.2.6-1 +- Package Spec generated @@ -0,0 +1 @@ +f2981952d01428eee2fecdfd06d44238 phylopypruner-1.2.6.tar.gz |