dotplot
Simple visualisation tool for sequences' similarity in bioinformatics
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
4 of 19 committers (21.1%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.8%) to scientific vocabulary
Keywords
Repository
Simple visualisation tool for sequences' similarity in bioinformatics
Basic Info
Statistics
- Stars: 13
- Watchers: 6
- Forks: 2
- Open Issues: 10
- Releases: 0
Topics
Metadata Files
README.md
Dotplot
Idea
Dotplot is a plot used mainly in biology for graphical visualisations of sequences' similarity. Read more on Wikipedia.
Why to create a new package?
There are many programs that attempt to create dotplots already. Unfortunately most of these programs was created long time ago and written in old versions of Java. This Python3 package will allow new generations of bioinformaticians to generate dotplots much easier.
Installation & usage
Instalation with pip
The easiest way to install this package with all dependencis is to use pip:
bash
pip install dotplot
Manual installation
bash
git clone https://github.com/kn-bibs/dotplot
To use graphical user interface, you will need to have pyqt5 installed, e.g. with:
python3
sudo apt-get install python3-pyqt5
To use matplotlib for drawing, you need to have it installed, e.g. with:
bash
sudo pip3 install matplotlib
Note: If you have chosen manual installation, use python3 dotplot command to run the program (while in the dotplot directory) instead of sole dotplot.
Basic usage
bash
dotplot --fasta 1.fa 2.fa
To use graphical user interface, type:
bash
dotplot --fasta 1.fa 2.fa --gui
You can also fetch sequences from various sources (at once):
bash
dotplot --gui --ncbi NP_001009852 --uniprot P03086
Advanced options
You can set window size to be used in plot creation:
bash
dotplot --fasta 1.fa 2.fa --gui --window_size 2
Furthermore, you can combine it with stringency:
bash
dotplot --fasta 1.fa 2.fa --gui --window_size 2 --stringency 2
And you can use a similarity matrix to compare aminoacids:
bash
dotplot --fasta 1.fa 2.fa --gui --window_size 2 --stringency 2 --matrix PAM120
Getting help
To access list of available options run command above with added option -h.
What will it do?
In the future our application will be able to read a wide range of input formats, and users will be able to parametrize alignment process and output format to their liking.
Dependencies & development
We are writing in Python3 and strict on code styling, with pep8 and pylint validation. We require all code merging to master to have at least 7,5 pylint score. To check this, at first install pytlint with pip3 and then, run the following command: python3 -m pylint dotplot.py, where in place of dotplot.py use any name of the module to be tested.
Owner
- Name: KN Bioinformatyki i Biologii Systemów
- Login: kn-bibs
- Kind: organization
- Location: Warsaw
- Website: http://bioinformatyka.mimuw.edu.pl/
- Repositories: 2
- Profile: https://github.com/kn-bibs
Koło Naukowe Bioinformatyki i Biologii Systemów Uniwersytetu Warszawskiego
GitHub Events
Total
Last Year
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| krassowski | k****l@g****m | 107 |
| kinga322 | k****a@k****l | 18 |
| Behoston | m****i@g****m | 12 |
| Bartek Henkiel | b****l@g****m | 11 |
| magickris93 | k****z@g****m | 8 |
| kinga322 | k****a@s****l | 7 |
| maciosz | a****k@s****l | 6 |
| Piotr Sliwa | p****a@g****m | 6 |
| Agreal1118 | a****1@g****m | 2 |
| Live System User | l****r@e****l | 2 |
| maryniak95 | m****5@g****m | 2 |
| sienkie | s****2@g****m | 1 |
| chmielowyzboj | r****a@g****m | 1 |
| rlatawiec | r****c@g****m | 1 |
| Ruta Misutyte | r****a@R****l | 1 |
| pjanek | p****3@s****l | 1 |
| szymek2137 | s****s@g****m | 1 |
| Xidron | m****i@s****l | 1 |
| vaira123 | v****s@w****l | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 29
- Total pull requests: 25
- Average time to close issues: about 1 month
- Average time to close pull requests: 5 days
- Total issue authors: 7
- Total pull request authors: 11
- Average comments per issue: 0.69
- Average comments per pull request: 0.68
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- krassowski (20)
- kinga322 (3)
- maciosz (2)
- Alria (1)
- magickris93 (1)
- kkuczkowska (1)
- pknut (1)
Pull Request Authors
- kinga322 (5)
- maciosz (5)
- krassowski (3)
- pjanek (3)
- Behoston (2)
- pasliwa (2)
- magickris93 (1)
- bartma11 (1)
- rmisutyte (1)
- szymek2137 (1)
- sienkie (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 9 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 5
- Total maintainers: 1
pypi.org: dotplot
Small bioinformatic package for dotplot's generation (in command line and in GUI)
- Homepage: https://github.com/kn-bibs/dotplot
- Documentation: https://dotplot.readthedocs.io/
- License: LGPL-3.0
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Latest release: 0.4.5
published over 8 years ago
Rankings
Maintainers (1)
Dependencies
- matplotlib *
- requests *
- PyQt5 *
- matplotlib *
- requests *