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%global _empty_manifest_terminate_build 0
Name: python-eggnog-mapper
Version: 2.1.11
Release: 1
Summary: Fast functional annotation of novel sequences using eggNOG orthology assignments.
License: GPLv3
URL: http://eggnog-mapper.embl.de
Source0: https://mirrors.aliyun.com/pypi/web/packages/7e/bc/f316df0761266c54b59fc1513d08486aeef68e02b61837375ed7113c8642/eggnog-mapper-2.1.11.tar.gz
BuildArch: noarch
Requires: python3-biopython
Requires: python3-psutil
Requires: python3-xlsxwriter
%description
[](https://travis-ci.com/eggnogdb/eggnog-mapper)
[](https://usegalaxy.eu/root?tool_id=eggnog_mapper)
# Overview
**EggNOG-mapper** is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.
Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence).
Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan [can be found here](https://github.com/jhcepas/emapper-benchmark/blob/master/benchmark_analysis.ipynb).
EggNOG-mapper is also available as a public online resource: http://eggnog-mapper.embl.de
# Documentation
https://github.com/jhcepas/eggnog-mapper/wiki
# Citation
If you use this software, please cite:
```
[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain
prediction at the metagenomic scale. Carlos P. Cantalapiedra,
Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021.
Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293
[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
orthology resource based on 5090 organisms and 2502 viruses. Jaime
Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia
K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars
J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8;
47(Database issue): D309–D314. doi: 10.1093/nar/gky1085
```
Please, cite also the underlying algorithm used for the search step of eggNOG-mapper, and Prodigal if it was used for gene prediction:
```
[HMMER] Accelerated Profile HMM Searches.
Eddy SR. 2011. PLoS Comput. Biol. 7:e1002195.
[DIAMOND] Sensitive protein alignments at tree-of-life scale using DIAMOND.
Buchfink B, Reuter K, Drost HG. 2021.
Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x
[MMSEQS2] MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.
Steinegger M & Söding J. 2017. Nat. Biotech. 35, 1026–1028. https://doi.org/10.1038/nbt.3988
[PRODIGAL] Prodigal: prokaryotic gene recognition and translation initiation site identification.
Hyatt et al. 2010. BMC Bioinformatics 11, 119. https://doi.org/10.1186/1471-2105-11-119.
```
%package -n python3-eggnog-mapper
Summary: Fast functional annotation of novel sequences using eggNOG orthology assignments.
Provides: python-eggnog-mapper
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-eggnog-mapper
[](https://travis-ci.com/eggnogdb/eggnog-mapper)
[](https://usegalaxy.eu/root?tool_id=eggnog_mapper)
# Overview
**EggNOG-mapper** is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.
Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence).
Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan [can be found here](https://github.com/jhcepas/emapper-benchmark/blob/master/benchmark_analysis.ipynb).
EggNOG-mapper is also available as a public online resource: http://eggnog-mapper.embl.de
# Documentation
https://github.com/jhcepas/eggnog-mapper/wiki
# Citation
If you use this software, please cite:
```
[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain
prediction at the metagenomic scale. Carlos P. Cantalapiedra,
Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021.
Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293
[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
orthology resource based on 5090 organisms and 2502 viruses. Jaime
Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia
K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars
J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8;
47(Database issue): D309–D314. doi: 10.1093/nar/gky1085
```
Please, cite also the underlying algorithm used for the search step of eggNOG-mapper, and Prodigal if it was used for gene prediction:
```
[HMMER] Accelerated Profile HMM Searches.
Eddy SR. 2011. PLoS Comput. Biol. 7:e1002195.
[DIAMOND] Sensitive protein alignments at tree-of-life scale using DIAMOND.
Buchfink B, Reuter K, Drost HG. 2021.
Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x
[MMSEQS2] MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.
Steinegger M & Söding J. 2017. Nat. Biotech. 35, 1026–1028. https://doi.org/10.1038/nbt.3988
[PRODIGAL] Prodigal: prokaryotic gene recognition and translation initiation site identification.
Hyatt et al. 2010. BMC Bioinformatics 11, 119. https://doi.org/10.1186/1471-2105-11-119.
```
%package help
Summary: Development documents and examples for eggnog-mapper
Provides: python3-eggnog-mapper-doc
%description help
[](https://travis-ci.com/eggnogdb/eggnog-mapper)
[](https://usegalaxy.eu/root?tool_id=eggnog_mapper)
# Overview
**EggNOG-mapper** is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.
Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs.
The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence).
Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan [can be found here](https://github.com/jhcepas/emapper-benchmark/blob/master/benchmark_analysis.ipynb).
EggNOG-mapper is also available as a public online resource: http://eggnog-mapper.embl.de
# Documentation
https://github.com/jhcepas/eggnog-mapper/wiki
# Citation
If you use this software, please cite:
```
[1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain
prediction at the metagenomic scale. Carlos P. Cantalapiedra,
Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021.
Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293
[2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated
orthology resource based on 5090 organisms and 2502 viruses. Jaime
Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia
K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars
J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8;
47(Database issue): D309–D314. doi: 10.1093/nar/gky1085
```
Please, cite also the underlying algorithm used for the search step of eggNOG-mapper, and Prodigal if it was used for gene prediction:
```
[HMMER] Accelerated Profile HMM Searches.
Eddy SR. 2011. PLoS Comput. Biol. 7:e1002195.
[DIAMOND] Sensitive protein alignments at tree-of-life scale using DIAMOND.
Buchfink B, Reuter K, Drost HG. 2021.
Nature Methods 18, 366–368 (2021). https://doi.org/10.1038/s41592-021-01101-x
[MMSEQS2] MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.
Steinegger M & Söding J. 2017. Nat. Biotech. 35, 1026–1028. https://doi.org/10.1038/nbt.3988
[PRODIGAL] Prodigal: prokaryotic gene recognition and translation initiation site identification.
Hyatt et al. 2010. BMC Bioinformatics 11, 119. https://doi.org/10.1186/1471-2105-11-119.
```
%prep
%autosetup -n eggnog-mapper-2.1.11
%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-eggnog-mapper -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 2.1.11-1
- Package Spec generated
|
