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https://github.com/art-egorov/svist4get
A simple visualisation tool for genomic tracks from sequencing experiments.
https://github.com/art-egorov/svist4get
bioinformatics ngs rna-seq visualisation
Last synced: about 1 month ago
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A simple visualisation tool for genomic tracks from sequencing experiments.
- Host: GitHub
- URL: https://github.com/art-egorov/svist4get
- Owner: art-egorov
- License: wtfpl
- Created: 2022-07-26T08:50:35.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2022-09-28T21:07:13.000Z (about 2 years ago)
- Last Synced: 2024-04-26T12:20:59.139Z (8 months ago)
- Topics: bioinformatics, ngs, rna-seq, visualisation
- Language: Python
- Homepage:
- Size: 7.39 MB
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
## Description
Svist4get is a simple bioinformatics tool for visualization of genomic signal tracks in user-defined genomic windows, either arbitrary selected by genomic coordinates or anchored to particular transcripts or genes.
**Supported genomic signal tracks:** bedGraph
**Supported genome annotation:** GTF (Ensembl or GENCODE)
**Supported output:** vector (pdf) and raster (png)
**Programming language:** Python 3
**OS:** Linux, Mac OS
**Python dependencies:** reportlab, statistics, biopython, configs, wand, argparse, pybedtools
**OS-level dependencies:** bedtools, ImageMagick (pdf-to-png conversion)
**License:** [WTFPL](http://www.wtfpl.net)
**Version:** 1.3.1 (July 2024)
**Note:** It's a new project's home page. It was moved from [bitbucket: artegorov/svist4get](https://bitbucket.org/artegorov/svist4get/src/master/). All new releases (starting with v. 1.3) of svist4get will be published only on this page (and pypi).
## Installation
You need those tools at the OS level (probably installable as Linux packages):
**bedtools** and **ImageMagick**
(Ubuntu users, please consult [FAQ](docs/FAQ.md) regarding possible issues with ImageMagick).
- The most stable release of svist4get can be installed directly from pypi:
```
python3 -m pip install svist4get
```
- The development version is available at github :
```
git clone https://github.com/art-egorov/svist4get.git
cd svist4get
python3 -m pip install --upgrade pip
python3 -m pip install wheel
python3 setup.py sdist bdist_wheel
python3 -m pip install .
```
## Contact
Please contact us by e-mail _artem**dot**egorov**AT**med**dot**lu**dot**se_ or use Issues to report any technical problems.
Old [Issues page](https://bitbucket.org/artegorov/svist4get/issues) from bitbucket.
## Image example
##### Console commands to reproduce the above image
```
svist4get --sampledata
```
```
svist4get -bg svist4get_data/RiboCov_cut.bedGraph svist4get_data/mRNACov_cut.bedGraph -gtf svist4get_data/S.cerevisiae.gtf -fa svist4get_data/S.cerevisiae.dna.fa -bl Ribo-Seq RNA-Seq -w I 108842 113506 -it "CCR4 and FUN26 genes" -rc -c A4_p1
```
## Reference
If you find svist4get useful, please cite:
Artyom A. Egorov, Ekaterina A. Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev and Ivan V. Kulakovskiy, **svist4get: a simple visualization tool for genomic tracks from sequencing experiments,** *BMC Bioinformatics, Volume 20, 2019, 113, [doi: 10.1186/s12859-019-2706-8](https://doi.org/10.1186/s12859-019-2706-8)*
## Detailed documentation
#### [Quickstart guide](docs/QSGUIDE.md)
#### [Command-line parameters](docs/PARAMETERS.md)
#### [Configuration file parameters](docs/CONFIG.md)
#### [API usage examples](docs/API.md)
#### [FAQ](docs/FAQ.md)
#### [Version log](docs/VERSION.md)
## Known issues
- Older versions of pybedtools (the necessary package) may fail to compile under Python 3.7. Usage of Python 3.6 is thus advised.
- GTF annotations other than Ensembl and GENCODE may be parsed incorrectly in some cases. Usage of those annotation sources is advised.
- pdf-to-png conversion may fail in some OS/ImageMagick combinations. Please consult [FAQ](docs/FAQ.md) for details.
## Authors
svist4get is developed by Artyom Egorov at the Laboratory of Systems Biology of Aging, MSU (Current address: [The Atkinson Lab](https://atkinson-lab.com), Department of Experimental Medical Science, Lund University). We are open for suggestions to extend and improve svist4get functionality. Please don't hesitate to share your ideas or feature requests.
*svist4get logo drawn by E. Kulakovskaya based on puppy named Cindy of [S. Anisimova](https://scholar.google.ru/citations?user=4GJj7S0AAAAJ&hl=en)
## Applications/Citations
More than 30 citations according to [Google Scholar](https://scholar.google.com/scholar?oi=bibs&hl=en&authuser=1&cites=8975441885381696257).