path: root/python-genegrouper.spec

%global _empty_manifest_terminate_build 0
Name:		python-GeneGrouper
Version:	1.0.3
Release:	1
Summary:	Find and cluster genomic regions containing a seed gene
License:	MIT License
URL:		https://github.com/agmcfarland/GeneGrouper
Source0:	https://mirrors.aliyun.com/pypi/web/packages/26/9b/a432e0124b851931e00c00871b667a06f318bc23c46edab6fb7eb24a6c64/GeneGrouper-1.0.3.tar.gz
BuildArch:	noarch


%description
<img src="docs/overview_figure.png" alt="GeneGrouper overview figure" width=1000>
[Why use GeneGrouper?](https://github.com/agmcfarland/GeneGrouper/wiki#what-is-genegrouper)
[See GeneGrouper tutorial](https://github.com/agmcfarland/GeneGrouper/wiki/GeneGrouper-tutorial-with-data)
[See GeneGrouper tutorial](https://github.com/agmcfarland/GeneGrouper/wiki/GeneGrouper-tutorial-with-data)
[See GeneGrouper outputs](https://github.com/agmcfarland/GeneGrouper/wiki/Output-file-descriptions)
[See FAQs](https://github.com/agmcfarland/GeneGrouper/wiki/Frequently-Asked-Questions)
# Installation
GeneGrouper can be installed using pip
```pip install GeneGrouper```
[GeneGrouper has multiple dependences.]((https://github.com/agmcfarland/GeneGrouper/wiki/Installation-and-dependencies#requirements-and-dependencies)) 
Follow the code below to create a self-contained conda environment for GeneGrouper. **Recommended**
**Installing Python and bioinformatic dependencies for grouping**
```
conda create -n GeneGrouper_env python=3.9
source activate GeneGrouper_env #or try: conda activate GeneGrouper_env
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
pip install biopython scipy scikit-learn pandas matplotlib GeneGrouper
conda install -c bioconda mcl blast mmseqs2 fasttree mafft
```
**Installing R and required packages for visualizations**
```
conda install -c conda-forge r-base=4.1.1 r-svglite r-reshape r-ggplot2 r-cowplot r-dplyr r-gggenes r-ape r-phytools r-BiocManager r-codetools
# enter R environment
R
# install additional packages from CRAN
install.packages('groupdata2',repos='https://cloud.r-project.org/', quiet=TRUE)
# install additional packages from 
BiocManager::install("ggtree")
# quit
q(save="no")
```
[For more information, see the installation wiki page](https://github.com/agmcfarland/GeneGrouper/wiki/Installation-and-dependencies)
# Inputs
### GeneGrouper has two required inputs:
1. A translated gene sequence in fasta format (with file extension .fasta/.txt)
2. A folder containing RefSeq GenBank-format genomes (with the file extension .gbff). [See instructions to download many RefSeq genomes at a time.](https://github.com/agmcfarland/GeneGrouper/wiki/Frequently-Asked-Questions#1-where-can-i-download-genbank-format-refseq-genomes-with-file-extension-gbff)
# Basic usage
#### Use `build_database` to make a GeneGrouper database of your RefSeq .gbff genomes
```
GeneGrouper -g /path/to/gbff -d /path/to/main_directory \
build_database
```
#### Use `find_regions` to search for regions containing a gene of interest and output to a search-specific directory
```
GeneGrouper -d /path/to/main_directory -n gene_search \
find_regions \
-f /path/to/query_gene.fasta
```
#### Use `visualize --visual_type main` to output visualizations of group gene architectures and their distribution within genomes and taxa
```
GeneGrouper -d /path/to/main_directory -n gene_search \
visualize \
--visual_type main
```
#### Use `visualize --visual_type group` to inspect a GeneGrouper group more closely. Replace <> with a group ID number.
```
GeneGrouper -d /path/to/main_directory -n gene_search \
visualize \
--visual_type group <>
```
#### Use `visualize --visual_type tree` to make a phylogenetic tree of each group's seed gene
```
GeneGrouper -d /path/to/main_directory -n gene_search \
visualize \
--visual_type tree
```
[See advanced usage examples](https://github.com/agmcfarland/GeneGrouper/wiki/Advanced-usage)
[See tutorial with provided example data](https://github.com/agmcfarland/GeneGrouper/wiki/GeneGrouper-tutorial-with-data)
# Outputs
 1. **For each search ```find_regions``` outputs:**
* **Four** tabular files with quantitative and qualitative descriptions of grouping results. 
* **One** fasta file containing all genes used in the analysis.
2. **For each search,  ```visualize --visual_type main``` outputs:**
* **Three** main visualizations provided.
3. **For each search, ```visualize --visual_type group \--group_label <n>``` outputs:**
* **One** additional visualization per group, where ```--group_label <n>``` has `<n>` replaced with the group number.  
* **Two** tabular files containing subgroup information for each ```--group_label <n>``` supplied.
4. **For each search, ```visualize --visual_type tree``` outputs:**
* **One** phylogenetic tree of each seed gene in each group.
[See complete output file descriptions](https://github.com/agmcfarland/GeneGrouper/wiki/Output-file-descriptions)
Each search and visualization will have the following file structure. Files under `visualizations` may differ.
```
├── main_directory
│   ├── search_results
│   │   ├── group_statistics_summmary.csv
│   │   ├── representative_group_member_summary.csv
│   │   ├── group_taxa_summary.csv
│   │   ├── group_regions.csv
│   │   ├── group_region_seqs.faa
│   │   ├── visualizations
│   │   │   ├── group_summary.png
│   │   │   ├── groups_by_taxa.png
│   │   │   ├── taxa_searched.png
│   │   │   ├── inspect_group_-1.png
│   │   │   ├── representative_seed_phylogeny.png
│   │   ├── internal_data
│   │   ├── subgroups
│   │   ├── seed_results.db
```
# Usage options
### Global flags
```
usage: GeneGrouper [-h] [-d] [-n] [-g] [-t]
                   {build_database,find_regions,visualize} ...
  -h, --help            show this help message and exit
  -d , --project_directory
                        Main directory to contain the base files used for
                        region searching and clustering. Default=current
                        directory.
  -n , --search_name    Name of the directory to contain search-specific
                        results. Default=region_search
  -g , --genomes_directory
                        Directory containing genbank-file format genomes with
                        the suffix .gbff. Default=./genomes.
  -t , --threads        Number of threads to use. Default=all threads.
```
### Subcommands
```
    build_database      Convert a set of genomes into a useable format for
                        GeneGrouper
    find_regions        Find regions given a translated gene and a set of
                        genomes
    visualize           Visualize GeneGrouper outputs. Three visualization options are provided.
                        Check the --visual_type help description.
```
### Subcommand flags
```build_database```
```
usage: GeneGrouper build_database [-h]
  -h, --help  show this help message and exit
```
```find_regions```
```
usage: GeneGrouper find_regions [-h] -f  [-us] [-ds] [-i] [-c] [-hk] [--min_group_size] [-re] [--force]
  -h, --help            show this help message and exit
  -f , --query_file     Provide the absolute path to a fasta file containing a translated gene sequence.
  -us , --upstream_search
                        Upstream search length in basepairs. Default=10000
  -ds , --downstream_search
                        Downstream search length in basepairs. Default=10000
  -i , --seed_identity
                        Identity cutoff for initial blast search. Default=60
  -c , --seed_coverage
                        Coverage cutoff for initial blast search. Default=90
  -hk , --seed_hits_kept
                        Number of blast hits to keep. Default=None
  --min_group_size
                        The minimum number of gene regions to constitute a group. Default=ln(jaccard distance length)
  -re , --recluster_iterations
                        Number of region re-clustering attempts after the initial clustering. Default=0
  --force               Flag to overwrite search name directory.
```
```visualize```
```
usage: GeneGrouper visualize [-h] [--visual_type] [--group_label]
  --visual_type      Choices: [main, group, tree]. Use main for main visualizations. Use group to
                     inspect specific group. Use tree for a phylogenetic tree of representative
                     seed sequencess. Default=main
  --group_label      The integer identifier of the group you wish to inspect. Default=-1
  --image_format     Choices: [png, svg]. Output image format. Use svg if you want to edit the
                     images. Default=png.
  --tip_label_type   Choices: [full, group]. Use full to include the sequence ID followed by group
                     ID. Use group to only have the group ID. Default=full
  --tip_label_size   Specify the tip label size in the output image. Default=2
```
# Citation
Alexander G McFarland, Nolan W Kennedy, Carolyn E Mills, Danielle Tullman-Ercek, Curtis Huttenhower, Erica M Hartmann, **Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper**, Bioinformatics, 2021;, btab752, https://doi.org/10.1093/bioinformatics/btab752
# Contact
Please message me at alexandermcfarland2022@u.northwestern.edu 
Follow me on twitter [@alexmcfarland_](https://twitter.com/alexmcfarland_)! 

%package -n python3-GeneGrouper
Summary:	Find and cluster genomic regions containing a seed gene
Provides:	python-GeneGrouper
BuildRequires:	python3-devel
BuildRequires:	python3-setuptools
BuildRequires:	python3-pip
%description -n python3-GeneGrouper
<img src="docs/overview_figure.png" alt="GeneGrouper overview figure" width=1000>
[Why use GeneGrouper?](https://github.com/agmcfarland/GeneGrouper/wiki#what-is-genegrouper)
[See GeneGrouper tutorial](https://github.com/agmcfarland/GeneGrouper/wiki/GeneGrouper-tutorial-with-data)
[See GeneGrouper tutorial](https://github.com/agmcfarland/GeneGrouper/wiki/GeneGrouper-tutorial-with-data)
[See GeneGrouper outputs](https://github.com/agmcfarland/GeneGrouper/wiki/Output-file-descriptions)
[See FAQs](https://github.com/agmcfarland/GeneGrouper/wiki/Frequently-Asked-Questions)
# Installation
GeneGrouper can be installed using pip
```pip install GeneGrouper```
[GeneGrouper has multiple dependences.]((https://github.com/agmcfarland/GeneGrouper/wiki/Installation-and-dependencies#requirements-and-dependencies)) 
Follow the code below to create a self-contained conda environment for GeneGrouper. **Recommended**
**Installing Python and bioinformatic dependencies for grouping**
```
conda create -n GeneGrouper_env python=3.9
source activate GeneGrouper_env #or try: conda activate GeneGrouper_env
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
pip install biopython scipy scikit-learn pandas matplotlib GeneGrouper
conda install -c bioconda mcl blast mmseqs2 fasttree mafft
```
**Installing R and required packages for visualizations**
```
conda install -c conda-forge r-base=4.1.1 r-svglite r-reshape r-ggplot2 r-cowplot r-dplyr r-gggenes r-ape r-phytools r-BiocManager r-codetools
# enter R environment
R
# install additional packages from CRAN
install.packages('groupdata2',repos='https://cloud.r-project.org/', quiet=TRUE)
# install additional packages from 
BiocManager::install("ggtree")
# quit
q(save="no")
```
[For more information, see the installation wiki page](https://github.com/agmcfarland/GeneGrouper/wiki/Installation-and-dependencies)
# Inputs
### GeneGrouper has two required inputs:
1. A translated gene sequence in fasta format (with file extension .fasta/.txt)
2. A folder containing RefSeq GenBank-format genomes (with the file extension .gbff). [See instructions to download many RefSeq genomes at a time.](https://github.com/agmcfarland/GeneGrouper/wiki/Frequently-Asked-Questions#1-where-can-i-download-genbank-format-refseq-genomes-with-file-extension-gbff)
# Basic usage
#### Use `build_database` to make a GeneGrouper database of your RefSeq .gbff genomes
```
GeneGrouper -g /path/to/gbff -d /path/to/main_directory \
build_database
```
#### Use `find_regions` to search for regions containing a gene of interest and output to a search-specific directory
```
GeneGrouper -d /path/to/main_directory -n gene_search \
find_regions \
-f /path/to/query_gene.fasta
```
#### Use `visualize --visual_type main` to output visualizations of group gene architectures and their distribution within genomes and taxa
```
GeneGrouper -d /path/to/main_directory -n gene_search \
visualize \
--visual_type main
```
#### Use `visualize --visual_type group` to inspect a GeneGrouper group more closely. Replace <> with a group ID number.
```
GeneGrouper -d /path/to/main_directory -n gene_search \
visualize \
--visual_type group <>
```
#### Use `visualize --visual_type tree` to make a phylogenetic tree of each group's seed gene
```
GeneGrouper -d /path/to/main_directory -n gene_search \
visualize \
--visual_type tree
```
[See advanced usage examples](https://github.com/agmcfarland/GeneGrouper/wiki/Advanced-usage)
[See tutorial with provided example data](https://github.com/agmcfarland/GeneGrouper/wiki/GeneGrouper-tutorial-with-data)
# Outputs
 1. **For each search ```find_regions``` outputs:**
* **Four** tabular files with quantitative and qualitative descriptions of grouping results. 
* **One** fasta file containing all genes used in the analysis.
2. **For each search,  ```visualize --visual_type main``` outputs:**
* **Three** main visualizations provided.
3. **For each search, ```visualize --visual_type group \--group_label <n>``` outputs:**
* **One** additional visualization per group, where ```--group_label <n>``` has `<n>` replaced with the group number.  
* **Two** tabular files containing subgroup information for each ```--group_label <n>``` supplied.
4. **For each search, ```visualize --visual_type tree``` outputs:**
* **One** phylogenetic tree of each seed gene in each group.
[See complete output file descriptions](https://github.com/agmcfarland/GeneGrouper/wiki/Output-file-descriptions)
Each search and visualization will have the following file structure. Files under `visualizations` may differ.
```
├── main_directory
│   ├── search_results
│   │   ├── group_statistics_summmary.csv
│   │   ├── representative_group_member_summary.csv
│   │   ├── group_taxa_summary.csv
│   │   ├── group_regions.csv
│   │   ├── group_region_seqs.faa
│   │   ├── visualizations
│   │   │   ├── group_summary.png
│   │   │   ├── groups_by_taxa.png
│   │   │   ├── taxa_searched.png
│   │   │   ├── inspect_group_-1.png
│   │   │   ├── representative_seed_phylogeny.png
│   │   ├── internal_data
│   │   ├── subgroups
│   │   ├── seed_results.db
```
# Usage options
### Global flags
```
usage: GeneGrouper [-h] [-d] [-n] [-g] [-t]
                   {build_database,find_regions,visualize} ...
  -h, --help            show this help message and exit
  -d , --project_directory
                        Main directory to contain the base files used for
                        region searching and clustering. Default=current
                        directory.
  -n , --search_name    Name of the directory to contain search-specific
                        results. Default=region_search
  -g , --genomes_directory
                        Directory containing genbank-file format genomes with
                        the suffix .gbff. Default=./genomes.
  -t , --threads        Number of threads to use. Default=all threads.
```
### Subcommands
```
    build_database      Convert a set of genomes into a useable format for
                        GeneGrouper
    find_regions        Find regions given a translated gene and a set of
                        genomes
    visualize           Visualize GeneGrouper outputs. Three visualization options are provided.
                        Check the --visual_type help description.
```
### Subcommand flags
```build_database```
```
usage: GeneGrouper build_database [-h]
  -h, --help  show this help message and exit
```
```find_regions```
```
usage: GeneGrouper find_regions [-h] -f  [-us] [-ds] [-i] [-c] [-hk] [--min_group_size] [-re] [--force]
  -h, --help            show this help message and exit
  -f , --query_file     Provide the absolute path to a fasta file containing a translated gene sequence.
  -us , --upstream_search
                        Upstream search length in basepairs. Default=10000
  -ds , --downstream_search
                        Downstream search length in basepairs. Default=10000
  -i , --seed_identity
                        Identity cutoff for initial blast search. Default=60
  -c , --seed_coverage
                        Coverage cutoff for initial blast search. Default=90
  -hk , --seed_hits_kept
                        Number of blast hits to keep. Default=None
  --min_group_size
                        The minimum number of gene regions to constitute a group. Default=ln(jaccard distance length)
  -re , --recluster_iterations
                        Number of region re-clustering attempts after the initial clustering. Default=0
  --force               Flag to overwrite search name directory.
```
```visualize```
```
usage: GeneGrouper visualize [-h] [--visual_type] [--group_label]
  --visual_type      Choices: [main, group, tree]. Use main for main visualizations. Use group to
                     inspect specific group. Use tree for a phylogenetic tree of representative
                     seed sequencess. Default=main
  --group_label      The integer identifier of the group you wish to inspect. Default=-1
  --image_format     Choices: [png, svg]. Output image format. Use svg if you want to edit the
                     images. Default=png.
  --tip_label_type   Choices: [full, group]. Use full to include the sequence ID followed by group
                     ID. Use group to only have the group ID. Default=full
  --tip_label_size   Specify the tip label size in the output image. Default=2
```
# Citation
Alexander G McFarland, Nolan W Kennedy, Carolyn E Mills, Danielle Tullman-Ercek, Curtis Huttenhower, Erica M Hartmann, **Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper**, Bioinformatics, 2021;, btab752, https://doi.org/10.1093/bioinformatics/btab752
# Contact
Please message me at alexandermcfarland2022@u.northwestern.edu 
Follow me on twitter [@alexmcfarland_](https://twitter.com/alexmcfarland_)! 

%package help
Summary:	Development documents and examples for GeneGrouper
Provides:	python3-GeneGrouper-doc
%description help
<img src="docs/overview_figure.png" alt="GeneGrouper overview figure" width=1000>
[Why use GeneGrouper?](https://github.com/agmcfarland/GeneGrouper/wiki#what-is-genegrouper)
[See GeneGrouper tutorial](https://github.com/agmcfarland/GeneGrouper/wiki/GeneGrouper-tutorial-with-data)
[See GeneGrouper tutorial](https://github.com/agmcfarland/GeneGrouper/wiki/GeneGrouper-tutorial-with-data)
[See GeneGrouper outputs](https://github.com/agmcfarland/GeneGrouper/wiki/Output-file-descriptions)
[See FAQs](https://github.com/agmcfarland/GeneGrouper/wiki/Frequently-Asked-Questions)
# Installation
GeneGrouper can be installed using pip
```pip install GeneGrouper```
[GeneGrouper has multiple dependences.]((https://github.com/agmcfarland/GeneGrouper/wiki/Installation-and-dependencies#requirements-and-dependencies)) 
Follow the code below to create a self-contained conda environment for GeneGrouper. **Recommended**
**Installing Python and bioinformatic dependencies for grouping**
```
conda create -n GeneGrouper_env python=3.9
source activate GeneGrouper_env #or try: conda activate GeneGrouper_env
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
pip install biopython scipy scikit-learn pandas matplotlib GeneGrouper
conda install -c bioconda mcl blast mmseqs2 fasttree mafft
```
**Installing R and required packages for visualizations**
```
conda install -c conda-forge r-base=4.1.1 r-svglite r-reshape r-ggplot2 r-cowplot r-dplyr r-gggenes r-ape r-phytools r-BiocManager r-codetools
# enter R environment
R
# install additional packages from CRAN
install.packages('groupdata2',repos='https://cloud.r-project.org/', quiet=TRUE)
# install additional packages from 
BiocManager::install("ggtree")
# quit
q(save="no")
```
[For more information, see the installation wiki page](https://github.com/agmcfarland/GeneGrouper/wiki/Installation-and-dependencies)
# Inputs
### GeneGrouper has two required inputs:
1. A translated gene sequence in fasta format (with file extension .fasta/.txt)
2. A folder containing RefSeq GenBank-format genomes (with the file extension .gbff). [See instructions to download many RefSeq genomes at a time.](https://github.com/agmcfarland/GeneGrouper/wiki/Frequently-Asked-Questions#1-where-can-i-download-genbank-format-refseq-genomes-with-file-extension-gbff)
# Basic usage
#### Use `build_database` to make a GeneGrouper database of your RefSeq .gbff genomes
```
GeneGrouper -g /path/to/gbff -d /path/to/main_directory \
build_database
```
#### Use `find_regions` to search for regions containing a gene of interest and output to a search-specific directory
```
GeneGrouper -d /path/to/main_directory -n gene_search \
find_regions \
-f /path/to/query_gene.fasta
```
#### Use `visualize --visual_type main` to output visualizations of group gene architectures and their distribution within genomes and taxa
```
GeneGrouper -d /path/to/main_directory -n gene_search \
visualize \
--visual_type main
```
#### Use `visualize --visual_type group` to inspect a GeneGrouper group more closely. Replace <> with a group ID number.
```
GeneGrouper -d /path/to/main_directory -n gene_search \
visualize \
--visual_type group <>
```
#### Use `visualize --visual_type tree` to make a phylogenetic tree of each group's seed gene
```
GeneGrouper -d /path/to/main_directory -n gene_search \
visualize \
--visual_type tree
```
[See advanced usage examples](https://github.com/agmcfarland/GeneGrouper/wiki/Advanced-usage)
[See tutorial with provided example data](https://github.com/agmcfarland/GeneGrouper/wiki/GeneGrouper-tutorial-with-data)
# Outputs
 1. **For each search ```find_regions``` outputs:**
* **Four** tabular files with quantitative and qualitative descriptions of grouping results. 
* **One** fasta file containing all genes used in the analysis.
2. **For each search,  ```visualize --visual_type main``` outputs:**
* **Three** main visualizations provided.
3. **For each search, ```visualize --visual_type group \--group_label <n>``` outputs:**
* **One** additional visualization per group, where ```--group_label <n>``` has `<n>` replaced with the group number.  
* **Two** tabular files containing subgroup information for each ```--group_label <n>``` supplied.
4. **For each search, ```visualize --visual_type tree``` outputs:**
* **One** phylogenetic tree of each seed gene in each group.
[See complete output file descriptions](https://github.com/agmcfarland/GeneGrouper/wiki/Output-file-descriptions)
Each search and visualization will have the following file structure. Files under `visualizations` may differ.
```
├── main_directory
│   ├── search_results
│   │   ├── group_statistics_summmary.csv
│   │   ├── representative_group_member_summary.csv
│   │   ├── group_taxa_summary.csv
│   │   ├── group_regions.csv
│   │   ├── group_region_seqs.faa
│   │   ├── visualizations
│   │   │   ├── group_summary.png
│   │   │   ├── groups_by_taxa.png
│   │   │   ├── taxa_searched.png
│   │   │   ├── inspect_group_-1.png
│   │   │   ├── representative_seed_phylogeny.png
│   │   ├── internal_data
│   │   ├── subgroups
│   │   ├── seed_results.db
```
# Usage options
### Global flags
```
usage: GeneGrouper [-h] [-d] [-n] [-g] [-t]
                   {build_database,find_regions,visualize} ...
  -h, --help            show this help message and exit
  -d , --project_directory
                        Main directory to contain the base files used for
                        region searching and clustering. Default=current
                        directory.
  -n , --search_name    Name of the directory to contain search-specific
                        results. Default=region_search
  -g , --genomes_directory
                        Directory containing genbank-file format genomes with
                        the suffix .gbff. Default=./genomes.
  -t , --threads        Number of threads to use. Default=all threads.
```
### Subcommands
```
    build_database      Convert a set of genomes into a useable format for
                        GeneGrouper
    find_regions        Find regions given a translated gene and a set of
                        genomes
    visualize           Visualize GeneGrouper outputs. Three visualization options are provided.
                        Check the --visual_type help description.
```
### Subcommand flags
```build_database```
```
usage: GeneGrouper build_database [-h]
  -h, --help  show this help message and exit
```
```find_regions```
```
usage: GeneGrouper find_regions [-h] -f  [-us] [-ds] [-i] [-c] [-hk] [--min_group_size] [-re] [--force]
  -h, --help            show this help message and exit
  -f , --query_file     Provide the absolute path to a fasta file containing a translated gene sequence.
  -us , --upstream_search
                        Upstream search length in basepairs. Default=10000
  -ds , --downstream_search
                        Downstream search length in basepairs. Default=10000
  -i , --seed_identity
                        Identity cutoff for initial blast search. Default=60
  -c , --seed_coverage
                        Coverage cutoff for initial blast search. Default=90
  -hk , --seed_hits_kept
                        Number of blast hits to keep. Default=None
  --min_group_size
                        The minimum number of gene regions to constitute a group. Default=ln(jaccard distance length)
  -re , --recluster_iterations
                        Number of region re-clustering attempts after the initial clustering. Default=0
  --force               Flag to overwrite search name directory.
```
```visualize```
```
usage: GeneGrouper visualize [-h] [--visual_type] [--group_label]
  --visual_type      Choices: [main, group, tree]. Use main for main visualizations. Use group to
                     inspect specific group. Use tree for a phylogenetic tree of representative
                     seed sequencess. Default=main
  --group_label      The integer identifier of the group you wish to inspect. Default=-1
  --image_format     Choices: [png, svg]. Output image format. Use svg if you want to edit the
                     images. Default=png.
  --tip_label_type   Choices: [full, group]. Use full to include the sequence ID followed by group
                     ID. Use group to only have the group ID. Default=full
  --tip_label_size   Specify the tip label size in the output image. Default=2
```
# Citation
Alexander G McFarland, Nolan W Kennedy, Carolyn E Mills, Danielle Tullman-Ercek, Curtis Huttenhower, Erica M Hartmann, **Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper**, Bioinformatics, 2021;, btab752, https://doi.org/10.1093/bioinformatics/btab752
# Contact
Please message me at alexandermcfarland2022@u.northwestern.edu 
Follow me on twitter [@alexmcfarland_](https://twitter.com/alexmcfarland_)! 

%prep
%autosetup -n GeneGrouper-1.0.3

%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-GeneGrouper -f filelist.lst
%dir %{python3_sitelib}/*

%files help -f doclist.lst
%{_docdir}/*

%changelog
* Tue Jun 20 2023 Python_Bot <Python_Bot@openeuler.org> - 1.0.3-1
- Package Spec generated