diff options
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-parebrick.spec | 275 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 277 insertions, 0 deletions
@@ -0,0 +1 @@ +/PaReBrick-0.5.5.tar.gz diff --git a/python-parebrick.spec b/python-parebrick.spec new file mode 100644 index 0000000..cb8631e --- /dev/null +++ b/python-parebrick.spec @@ -0,0 +1,275 @@ +%global _empty_manifest_terminate_build 0 +Name: python-PaReBrick +Version: 0.5.5 +Release: 1 +Summary: A bioinf tool for finding genome rearrangements in bacterial genomes +License: MIT License +URL: https://github.com/ctlab/parallel-rearrangements +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/1c/b0/aa7ca2816231fe1e7f9bc65fabe65ec1e1214c51c41bdfec25124f5b52e7/PaReBrick-0.5.5.tar.gz +BuildArch: noarch + +Requires: python3-PyQt5 +Requires: python3-ete3 +Requires: python3-scikit-learn +Requires: python3-seaborn +Requires: python3-bg + +%description +## Motivation +High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. +Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. +Specifically, such rearrangements might be responsible for virulence, antibiotic resistance, and antigenic variation. +However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. +## Methods and Results + +We present **tool `PaReBrick`** — implementation of an algorithmic solution for the identification of parallel rearrangements in bacterial population. +We define the term "parallel rearrangements" as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. +The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. +It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. +The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. +We [demonstrated](https://doi.org/10.1093/bioinformatics/btab691) PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. +## Installation +PaReBrick can be installed with `pip`: +```bash +pip install PaReBrick +``` +Now you can run tool from any directory as `PaReBrick` (or `parebrick`). +## Script parameters +Main script of project including all modules together can be run from anywhere as console tool. +### Required input +**Important for input:** Identifiers in tree and on in blocks must be equal; +#### `--tree/t` +Tree in newick format, must be parsable by ete3 library. +You can read more about [formats supported by ete3](http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-and-writing-newick-trees) +#### `--blocks_folder/-b` +Path to folder with blocks resulted as output of original Sibelia or maf2synteny tool. +[BLOCKS-OBTAIN.md](BLOCKS-OBTAIN.md) — instruction about how to obtain synteny blocks using SibeliaZ. +### Optional input +#### `--labels/-l` +Path to csv file with tree labels for showing on phylogenetic tree. +Must contain two columns: `strain` and `label`. +#### `--output/-o` +Path to output folder. +Default is `./parebrick_output` +### Output +Output consist of tree folders. +1. `preprocessed_data` — +here you can find both all and common synteny blocks in both `infercars`, `GRIMM` and `csv` formats. +As well as same `genomes_lengths.csv` file with lengths of provided genomes. +2. `balanced_rearrangements_output` — this folder contains `stats.csv` file with all non-convex characters statistics of balanced rearrangements. +And folders `characters`, `tree_colorings` with character representation in rendered `.pdf` tree and `.csv` formats. +3. `unbalanced_rearrangements_output` — this folder contains `stats.csv` file with all non-convex characters statistics of unbalanced rearrangements. +And folders `characters`, `tree_colorings` with character in rendered `.pdf` tree and `.csv` formats in subfolders according to their clustering representation. +## Example run and data +Example data is available in `example-data` folder. +### How to run example: +1. Clone all repository with data: +```bash +git clone https://github.com/ctlab/parallel-rearrangements +``` +2. Change directory to data folder: +```bash +cd parallel-rearrangements/example-data/streptococcus_pyogenes +``` +3. (a) Running tool on example input: +``` +PaReBrick -t input/tree.nwk -b input/maf2synteny-output -l input/labels.csv +``` +3. (b) Or with minimal required arguments (no labels): +``` +PaReBrick -t input/tree.nwk -b input/maf2synteny-output +``` +## Citation +If you use `PaReBrick` in your research, please cite: +Alexey Zabelkin, Yulia Yakovleva, Olga Bochkareva, Nikita Alexeev, PaReBrick: PArallel REarrangements and BReaks identification toolkit, Bioinformatics, 2021; btab691, https://doi.org/10.1093/bioinformatics/btab691 + +%package -n python3-PaReBrick +Summary: A bioinf tool for finding genome rearrangements in bacterial genomes +Provides: python-PaReBrick +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-PaReBrick +## Motivation +High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. +Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. +Specifically, such rearrangements might be responsible for virulence, antibiotic resistance, and antigenic variation. +However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. +## Methods and Results + +We present **tool `PaReBrick`** — implementation of an algorithmic solution for the identification of parallel rearrangements in bacterial population. +We define the term "parallel rearrangements" as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. +The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. +It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. +The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. +We [demonstrated](https://doi.org/10.1093/bioinformatics/btab691) PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. +## Installation +PaReBrick can be installed with `pip`: +```bash +pip install PaReBrick +``` +Now you can run tool from any directory as `PaReBrick` (or `parebrick`). +## Script parameters +Main script of project including all modules together can be run from anywhere as console tool. +### Required input +**Important for input:** Identifiers in tree and on in blocks must be equal; +#### `--tree/t` +Tree in newick format, must be parsable by ete3 library. +You can read more about [formats supported by ete3](http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-and-writing-newick-trees) +#### `--blocks_folder/-b` +Path to folder with blocks resulted as output of original Sibelia or maf2synteny tool. +[BLOCKS-OBTAIN.md](BLOCKS-OBTAIN.md) — instruction about how to obtain synteny blocks using SibeliaZ. +### Optional input +#### `--labels/-l` +Path to csv file with tree labels for showing on phylogenetic tree. +Must contain two columns: `strain` and `label`. +#### `--output/-o` +Path to output folder. +Default is `./parebrick_output` +### Output +Output consist of tree folders. +1. `preprocessed_data` — +here you can find both all and common synteny blocks in both `infercars`, `GRIMM` and `csv` formats. +As well as same `genomes_lengths.csv` file with lengths of provided genomes. +2. `balanced_rearrangements_output` — this folder contains `stats.csv` file with all non-convex characters statistics of balanced rearrangements. +And folders `characters`, `tree_colorings` with character representation in rendered `.pdf` tree and `.csv` formats. +3. `unbalanced_rearrangements_output` — this folder contains `stats.csv` file with all non-convex characters statistics of unbalanced rearrangements. +And folders `characters`, `tree_colorings` with character in rendered `.pdf` tree and `.csv` formats in subfolders according to their clustering representation. +## Example run and data +Example data is available in `example-data` folder. +### How to run example: +1. Clone all repository with data: +```bash +git clone https://github.com/ctlab/parallel-rearrangements +``` +2. Change directory to data folder: +```bash +cd parallel-rearrangements/example-data/streptococcus_pyogenes +``` +3. (a) Running tool on example input: +``` +PaReBrick -t input/tree.nwk -b input/maf2synteny-output -l input/labels.csv +``` +3. (b) Or with minimal required arguments (no labels): +``` +PaReBrick -t input/tree.nwk -b input/maf2synteny-output +``` +## Citation +If you use `PaReBrick` in your research, please cite: +Alexey Zabelkin, Yulia Yakovleva, Olga Bochkareva, Nikita Alexeev, PaReBrick: PArallel REarrangements and BReaks identification toolkit, Bioinformatics, 2021; btab691, https://doi.org/10.1093/bioinformatics/btab691 + +%package help +Summary: Development documents and examples for PaReBrick +Provides: python3-PaReBrick-doc +%description help +## Motivation +High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. +Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. +Specifically, such rearrangements might be responsible for virulence, antibiotic resistance, and antigenic variation. +However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. +## Methods and Results + +We present **tool `PaReBrick`** — implementation of an algorithmic solution for the identification of parallel rearrangements in bacterial population. +We define the term "parallel rearrangements" as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. +The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. +It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. +The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. +We [demonstrated](https://doi.org/10.1093/bioinformatics/btab691) PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. +## Installation +PaReBrick can be installed with `pip`: +```bash +pip install PaReBrick +``` +Now you can run tool from any directory as `PaReBrick` (or `parebrick`). +## Script parameters +Main script of project including all modules together can be run from anywhere as console tool. +### Required input +**Important for input:** Identifiers in tree and on in blocks must be equal; +#### `--tree/t` +Tree in newick format, must be parsable by ete3 library. +You can read more about [formats supported by ete3](http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-and-writing-newick-trees) +#### `--blocks_folder/-b` +Path to folder with blocks resulted as output of original Sibelia or maf2synteny tool. +[BLOCKS-OBTAIN.md](BLOCKS-OBTAIN.md) — instruction about how to obtain synteny blocks using SibeliaZ. +### Optional input +#### `--labels/-l` +Path to csv file with tree labels for showing on phylogenetic tree. +Must contain two columns: `strain` and `label`. +#### `--output/-o` +Path to output folder. +Default is `./parebrick_output` +### Output +Output consist of tree folders. +1. `preprocessed_data` — +here you can find both all and common synteny blocks in both `infercars`, `GRIMM` and `csv` formats. +As well as same `genomes_lengths.csv` file with lengths of provided genomes. +2. `balanced_rearrangements_output` — this folder contains `stats.csv` file with all non-convex characters statistics of balanced rearrangements. +And folders `characters`, `tree_colorings` with character representation in rendered `.pdf` tree and `.csv` formats. +3. `unbalanced_rearrangements_output` — this folder contains `stats.csv` file with all non-convex characters statistics of unbalanced rearrangements. +And folders `characters`, `tree_colorings` with character in rendered `.pdf` tree and `.csv` formats in subfolders according to their clustering representation. +## Example run and data +Example data is available in `example-data` folder. +### How to run example: +1. Clone all repository with data: +```bash +git clone https://github.com/ctlab/parallel-rearrangements +``` +2. Change directory to data folder: +```bash +cd parallel-rearrangements/example-data/streptococcus_pyogenes +``` +3. (a) Running tool on example input: +``` +PaReBrick -t input/tree.nwk -b input/maf2synteny-output -l input/labels.csv +``` +3. (b) Or with minimal required arguments (no labels): +``` +PaReBrick -t input/tree.nwk -b input/maf2synteny-output +``` +## Citation +If you use `PaReBrick` in your research, please cite: +Alexey Zabelkin, Yulia Yakovleva, Olga Bochkareva, Nikita Alexeev, PaReBrick: PArallel REarrangements and BReaks identification toolkit, Bioinformatics, 2021; btab691, https://doi.org/10.1093/bioinformatics/btab691 + +%prep +%autosetup -n PaReBrick-0.5.5 + +%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-PaReBrick -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Fri May 05 2023 Python_Bot <Python_Bot@openeuler.org> - 0.5.5-1 +- Package Spec generated @@ -0,0 +1 @@ +0b8540a6f2aef001d08fdf41bb59b45b PaReBrick-0.5.5.tar.gz |