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|
%global _empty_manifest_terminate_build 0
Name: python-Vicinator
Version: 0.0.32
Release: 1
Summary: A small python package to trace orthology neighborhood across feature files
License: MIT License
URL: https://github.com/ba1/vicinator
Source0: https://mirrors.aliyun.com/pypi/web/packages/fb/20/1bc6dd3bc088bfdd933b1ace6c2a384c7da34491dc54d7f2907621d2b01f/Vicinator-0.0.32.tar.gz
BuildArch: noarch
Requires: python3-ete3
Requires: python3-ansi2html
Requires: python3-colorama
Requires: python3-pandas
Requires: python3-importlib-metadata
%description
[](https://www.travis-ci.org/ba1/Vicinator)
[](https://codecov.io/gh/ba1/Vicinator)
[](https://badge.fury.io/py/Vicinator)
[](https://requires.io/github/ba1/Vicinator/requirements/?branch=master)
[](https://vicinator.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/psf/black)
# Vicinator
### What is Vicinator for?
Vicinator visualizes the microsynteny of grouped proteins (e.g. orthologs) across a large collection of genomes.
As input, it requires a mapping of the genomes' proteins to the respective protein groups and a directory containing
the genomes' feature files, i.e. files of the format *\*.gff* or *\*_feature_table.txt*.
### What is Vicinator not for?
As stated above, Vicinator relies on a pre-computed grouping of proteins across genomes. It can not find these
groups of genes for you.
### Installation
Vicinator is written for Python 3.6+
It is recommended to install Vicinator inside a virtual environment, e.g. with venv:
`python3 -m venv myenv`
This activates the new environment called *myenv*. While activated, you can install the latest version via pip.
The following command installs the latest version and all unmet requirements automatically.
`pip install --upgrades vicinator`
Requirements:
- ansi2html>=1.5.2
- colorama>=0.4.4
- ete3>=3.1.2
- pandas>=1.1.3
- importlib-metadata>=3.1.1
- setuptools-scm>=5.0.1
### Options
```
python3 vicinator/vicinator.py --help
usage: vicinator [-h] --tabular-ortholog-groups <orthology_table> --feat-tables-dir <dir_path>
--reference <file_path> --centerprotein-accession <str>
(--extension-size <int> | --extension-mask <int> [<int> ...])
[--tree <newick_tree_file_path>] [--outdir <dir_path>] [--prefix <str>]
[--outputlabel-map <file_path>] [--nprocs <int>] [--force] [--version]
Track Microsynteny of target proteins and its orthologs across genomes.
required arguments:
--tabular-ortholog-groups <orthology_table>
path to mapping file with format
ortholog_group_id<tab>genome_id<tab>protein_seq_id
--feat-tables-dir <dir_path>
path to directory of *.feature_tables.txt or *.gff3 files that shall be
screen
required arguments (neighborhood):
--reference <file_path>
path to a ncbi style feature table or gff file that acts as a reference
--centerprotein-accession <str>
unique identifier of the central gene of the window
--extension-size <int>
defines the #features that are co-checked to the left and right of the
centerprotein
--extension-mask <int> [<int> ...]
defines the position of features that are co-checked to the left and right
relative to the centerprotein (position 0).
optional arguments (output):
--tree <newick_tree_file_path>
path to newick tree that includes all taxa to be screened
--outdir <dir_path> path to desired output directory
--prefix <str> if option is set, shows intergenic distances of genes surrounding the
center gene
--outputlabel-map <file_path>
Attempts to replace genome accessions in the outputs with a replacement
string. Requires a two-column map file formatted like so: 'genome file
accession' <tab> 'replacement string'. The replacement will automatically
be cut to a maximum of 30 chars.
optional arguments (run):
--nprocs <int> Number of CPUs for parallel processing of genomes. Default: Number of
CPUs-1
--force if option is set, existing ortholog databases in the output dir are
ignored and will be overwritten
```
### Input: Required Arguments
<br/>
`--tabular-ortholog-groups <orthology_table>`
>Vicinator requires a tab-separated three-column mapping of orthologs that is formatted like so:
>
> **group_id** \tab **genome_id** \tab **protein_id**
> 
<br/>
` --feat-tables-dir <dir_path>`
>Vicinator expects the path to a directory containing *.gff* format or *_feature_table.txt*
> files of all the genomes you want to trace the microsynteny in.
>
> A recommended source for these files is NCBI RefSeq. In order for the mapping to work, the filenames
> should correspond to the **genome_ids** specified in the mapping file:
>
> E.g. line 7: **OG_2 genomeB protein_X011**
> <br/>
> triggers a search in a feature file named **genomeB.gff** or **genomeB_genomic.gff** or **genomeB_feature_table.txt**
> in the directory specified with `--feat-tables-dir`. Effectively, it tries to locate the protein_X011 in this feature file.
<br/>
`--reference <file_path>`
> the path to a reference genome feature file where the center-protein accession must be found
<br/>
`--centerprotein-accession` & `--extension-size <int>`
>Identifies the window of vicinity around a center-protein which is traced based on the findings in the reference
> genome.
> 
<br/>
## Example Basic Usage
`vicinator --tabular-ortholog-groups orthogenome_map.tsv --feat-tables-dir ./gff_dir --outdir ./results --reference gff_dir/MUSMU@10090@1.gff --centerprotein XP_006539605.1 --extension-size 3`
## Example Advanced Usage
When vicinator receives a phylogenetic tree (with genome_ids as leaf labels) it will trace the microsynteny in order of
increasing phylogentic distance to the reference genome specified.
`vicinator --tabular-ortholog-groups orthogenome_map.tsv --feat-tables-dir ./gff_dir --outdir ./results --reference gff_dir/MUSMU@10090@1.gff --centerprotein XP_006539605.1 --extension-size 3 --tree phylogeny.nwk`
## Example Advanced Usage 2
When vicinator is started with the `--extension-mask` parameter it excpects a space-separated list of integers representing
the relative positions of proteins to the center-protein vicinator will trace. You don't have to give
them in order since they will be sorted automatically with 0 representing the center protein (always included).
`vicinator --tabular-ortholog-groups orthogenome_map.tsv --feat-tables-dir ./gff_dir --outdir ./results --reference gff_dir/MUSMU@10090@1.gff --centerprotein XP_006539605.1 --extension-mask -35 -1 0 7 9`
%package -n python3-Vicinator
Summary: A small python package to trace orthology neighborhood across feature files
Provides: python-Vicinator
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-Vicinator
[](https://www.travis-ci.org/ba1/Vicinator)
[](https://codecov.io/gh/ba1/Vicinator)
[](https://badge.fury.io/py/Vicinator)
[](https://requires.io/github/ba1/Vicinator/requirements/?branch=master)
[](https://vicinator.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/psf/black)
# Vicinator
### What is Vicinator for?
Vicinator visualizes the microsynteny of grouped proteins (e.g. orthologs) across a large collection of genomes.
As input, it requires a mapping of the genomes' proteins to the respective protein groups and a directory containing
the genomes' feature files, i.e. files of the format *\*.gff* or *\*_feature_table.txt*.
### What is Vicinator not for?
As stated above, Vicinator relies on a pre-computed grouping of proteins across genomes. It can not find these
groups of genes for you.
### Installation
Vicinator is written for Python 3.6+
It is recommended to install Vicinator inside a virtual environment, e.g. with venv:
`python3 -m venv myenv`
This activates the new environment called *myenv*. While activated, you can install the latest version via pip.
The following command installs the latest version and all unmet requirements automatically.
`pip install --upgrades vicinator`
Requirements:
- ansi2html>=1.5.2
- colorama>=0.4.4
- ete3>=3.1.2
- pandas>=1.1.3
- importlib-metadata>=3.1.1
- setuptools-scm>=5.0.1
### Options
```
python3 vicinator/vicinator.py --help
usage: vicinator [-h] --tabular-ortholog-groups <orthology_table> --feat-tables-dir <dir_path>
--reference <file_path> --centerprotein-accession <str>
(--extension-size <int> | --extension-mask <int> [<int> ...])
[--tree <newick_tree_file_path>] [--outdir <dir_path>] [--prefix <str>]
[--outputlabel-map <file_path>] [--nprocs <int>] [--force] [--version]
Track Microsynteny of target proteins and its orthologs across genomes.
required arguments:
--tabular-ortholog-groups <orthology_table>
path to mapping file with format
ortholog_group_id<tab>genome_id<tab>protein_seq_id
--feat-tables-dir <dir_path>
path to directory of *.feature_tables.txt or *.gff3 files that shall be
screen
required arguments (neighborhood):
--reference <file_path>
path to a ncbi style feature table or gff file that acts as a reference
--centerprotein-accession <str>
unique identifier of the central gene of the window
--extension-size <int>
defines the #features that are co-checked to the left and right of the
centerprotein
--extension-mask <int> [<int> ...]
defines the position of features that are co-checked to the left and right
relative to the centerprotein (position 0).
optional arguments (output):
--tree <newick_tree_file_path>
path to newick tree that includes all taxa to be screened
--outdir <dir_path> path to desired output directory
--prefix <str> if option is set, shows intergenic distances of genes surrounding the
center gene
--outputlabel-map <file_path>
Attempts to replace genome accessions in the outputs with a replacement
string. Requires a two-column map file formatted like so: 'genome file
accession' <tab> 'replacement string'. The replacement will automatically
be cut to a maximum of 30 chars.
optional arguments (run):
--nprocs <int> Number of CPUs for parallel processing of genomes. Default: Number of
CPUs-1
--force if option is set, existing ortholog databases in the output dir are
ignored and will be overwritten
```
### Input: Required Arguments
<br/>
`--tabular-ortholog-groups <orthology_table>`
>Vicinator requires a tab-separated three-column mapping of orthologs that is formatted like so:
>
> **group_id** \tab **genome_id** \tab **protein_id**
> 
<br/>
` --feat-tables-dir <dir_path>`
>Vicinator expects the path to a directory containing *.gff* format or *_feature_table.txt*
> files of all the genomes you want to trace the microsynteny in.
>
> A recommended source for these files is NCBI RefSeq. In order for the mapping to work, the filenames
> should correspond to the **genome_ids** specified in the mapping file:
>
> E.g. line 7: **OG_2 genomeB protein_X011**
> <br/>
> triggers a search in a feature file named **genomeB.gff** or **genomeB_genomic.gff** or **genomeB_feature_table.txt**
> in the directory specified with `--feat-tables-dir`. Effectively, it tries to locate the protein_X011 in this feature file.
<br/>
`--reference <file_path>`
> the path to a reference genome feature file where the center-protein accession must be found
<br/>
`--centerprotein-accession` & `--extension-size <int>`
>Identifies the window of vicinity around a center-protein which is traced based on the findings in the reference
> genome.
> 
<br/>
## Example Basic Usage
`vicinator --tabular-ortholog-groups orthogenome_map.tsv --feat-tables-dir ./gff_dir --outdir ./results --reference gff_dir/MUSMU@10090@1.gff --centerprotein XP_006539605.1 --extension-size 3`
## Example Advanced Usage
When vicinator receives a phylogenetic tree (with genome_ids as leaf labels) it will trace the microsynteny in order of
increasing phylogentic distance to the reference genome specified.
`vicinator --tabular-ortholog-groups orthogenome_map.tsv --feat-tables-dir ./gff_dir --outdir ./results --reference gff_dir/MUSMU@10090@1.gff --centerprotein XP_006539605.1 --extension-size 3 --tree phylogeny.nwk`
## Example Advanced Usage 2
When vicinator is started with the `--extension-mask` parameter it excpects a space-separated list of integers representing
the relative positions of proteins to the center-protein vicinator will trace. You don't have to give
them in order since they will be sorted automatically with 0 representing the center protein (always included).
`vicinator --tabular-ortholog-groups orthogenome_map.tsv --feat-tables-dir ./gff_dir --outdir ./results --reference gff_dir/MUSMU@10090@1.gff --centerprotein XP_006539605.1 --extension-mask -35 -1 0 7 9`
%package help
Summary: Development documents and examples for Vicinator
Provides: python3-Vicinator-doc
%description help
[](https://www.travis-ci.org/ba1/Vicinator)
[](https://codecov.io/gh/ba1/Vicinator)
[](https://badge.fury.io/py/Vicinator)
[](https://requires.io/github/ba1/Vicinator/requirements/?branch=master)
[](https://vicinator.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/psf/black)
# Vicinator
### What is Vicinator for?
Vicinator visualizes the microsynteny of grouped proteins (e.g. orthologs) across a large collection of genomes.
As input, it requires a mapping of the genomes' proteins to the respective protein groups and a directory containing
the genomes' feature files, i.e. files of the format *\*.gff* or *\*_feature_table.txt*.
### What is Vicinator not for?
As stated above, Vicinator relies on a pre-computed grouping of proteins across genomes. It can not find these
groups of genes for you.
### Installation
Vicinator is written for Python 3.6+
It is recommended to install Vicinator inside a virtual environment, e.g. with venv:
`python3 -m venv myenv`
This activates the new environment called *myenv*. While activated, you can install the latest version via pip.
The following command installs the latest version and all unmet requirements automatically.
`pip install --upgrades vicinator`
Requirements:
- ansi2html>=1.5.2
- colorama>=0.4.4
- ete3>=3.1.2
- pandas>=1.1.3
- importlib-metadata>=3.1.1
- setuptools-scm>=5.0.1
### Options
```
python3 vicinator/vicinator.py --help
usage: vicinator [-h] --tabular-ortholog-groups <orthology_table> --feat-tables-dir <dir_path>
--reference <file_path> --centerprotein-accession <str>
(--extension-size <int> | --extension-mask <int> [<int> ...])
[--tree <newick_tree_file_path>] [--outdir <dir_path>] [--prefix <str>]
[--outputlabel-map <file_path>] [--nprocs <int>] [--force] [--version]
Track Microsynteny of target proteins and its orthologs across genomes.
required arguments:
--tabular-ortholog-groups <orthology_table>
path to mapping file with format
ortholog_group_id<tab>genome_id<tab>protein_seq_id
--feat-tables-dir <dir_path>
path to directory of *.feature_tables.txt or *.gff3 files that shall be
screen
required arguments (neighborhood):
--reference <file_path>
path to a ncbi style feature table or gff file that acts as a reference
--centerprotein-accession <str>
unique identifier of the central gene of the window
--extension-size <int>
defines the #features that are co-checked to the left and right of the
centerprotein
--extension-mask <int> [<int> ...]
defines the position of features that are co-checked to the left and right
relative to the centerprotein (position 0).
optional arguments (output):
--tree <newick_tree_file_path>
path to newick tree that includes all taxa to be screened
--outdir <dir_path> path to desired output directory
--prefix <str> if option is set, shows intergenic distances of genes surrounding the
center gene
--outputlabel-map <file_path>
Attempts to replace genome accessions in the outputs with a replacement
string. Requires a two-column map file formatted like so: 'genome file
accession' <tab> 'replacement string'. The replacement will automatically
be cut to a maximum of 30 chars.
optional arguments (run):
--nprocs <int> Number of CPUs for parallel processing of genomes. Default: Number of
CPUs-1
--force if option is set, existing ortholog databases in the output dir are
ignored and will be overwritten
```
### Input: Required Arguments
<br/>
`--tabular-ortholog-groups <orthology_table>`
>Vicinator requires a tab-separated three-column mapping of orthologs that is formatted like so:
>
> **group_id** \tab **genome_id** \tab **protein_id**
> 
<br/>
` --feat-tables-dir <dir_path>`
>Vicinator expects the path to a directory containing *.gff* format or *_feature_table.txt*
> files of all the genomes you want to trace the microsynteny in.
>
> A recommended source for these files is NCBI RefSeq. In order for the mapping to work, the filenames
> should correspond to the **genome_ids** specified in the mapping file:
>
> E.g. line 7: **OG_2 genomeB protein_X011**
> <br/>
> triggers a search in a feature file named **genomeB.gff** or **genomeB_genomic.gff** or **genomeB_feature_table.txt**
> in the directory specified with `--feat-tables-dir`. Effectively, it tries to locate the protein_X011 in this feature file.
<br/>
`--reference <file_path>`
> the path to a reference genome feature file where the center-protein accession must be found
<br/>
`--centerprotein-accession` & `--extension-size <int>`
>Identifies the window of vicinity around a center-protein which is traced based on the findings in the reference
> genome.
> 
<br/>
## Example Basic Usage
`vicinator --tabular-ortholog-groups orthogenome_map.tsv --feat-tables-dir ./gff_dir --outdir ./results --reference gff_dir/MUSMU@10090@1.gff --centerprotein XP_006539605.1 --extension-size 3`
## Example Advanced Usage
When vicinator receives a phylogenetic tree (with genome_ids as leaf labels) it will trace the microsynteny in order of
increasing phylogentic distance to the reference genome specified.
`vicinator --tabular-ortholog-groups orthogenome_map.tsv --feat-tables-dir ./gff_dir --outdir ./results --reference gff_dir/MUSMU@10090@1.gff --centerprotein XP_006539605.1 --extension-size 3 --tree phylogeny.nwk`
## Example Advanced Usage 2
When vicinator is started with the `--extension-mask` parameter it excpects a space-separated list of integers representing
the relative positions of proteins to the center-protein vicinator will trace. You don't have to give
them in order since they will be sorted automatically with 0 representing the center protein (always included).
`vicinator --tabular-ortholog-groups orthogenome_map.tsv --feat-tables-dir ./gff_dir --outdir ./results --reference gff_dir/MUSMU@10090@1.gff --centerprotein XP_006539605.1 --extension-mask -35 -1 0 7 9`
%prep
%autosetup -n Vicinator-0.0.32
%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-Vicinator -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Fri Jun 09 2023 Python_Bot <Python_Bot@openeuler.org> - 0.0.32-1
- Package Spec generated
|
