svist4get 1.3.1.1

A simple visualization tool for genomic tracks from sequencing experiments

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
Version: 1.3.1 (July 2024)

Note: It's a new project's home page. It was moved from bitbucket: artegorov/svist4get. 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 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 artemdotegorovATmeddotludotse or use Issues to report any technical problems.
Old Issues page 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

Detailed documentation

Quickstart guide

Command-line parameters

Configuration file parameters

API usage examples

FAQ

Version log

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 for details.

Authors

svist4get is developed by Artyom Egorov at the Laboratory of Systems Biology of Aging, MSU (Current address: The Atkinson Lab, 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

Applications/Citations

More than 30 citations according to Google Scholar.