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https://github.com/ebedthan/fastchaos
(Integer) chaos game representation for DNA sequences
https://github.com/ebedthan/fastchaos
bioinformatics chaos-game-representation integer-chaos-game-representation rust
Last synced: about 1 month ago
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(Integer) chaos game representation for DNA sequences
- Host: GitHub
- URL: https://github.com/ebedthan/fastchaos
- Owner: Ebedthan
- License: mit
- Created: 2022-04-15T12:54:06.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-04-03T21:49:12.000Z (8 months ago)
- Last Synced: 2024-04-03T22:34:59.415Z (8 months ago)
- Topics: bioinformatics, chaos-game-representation, integer-chaos-game-representation, rust
- Language: Rust
- Homepage:
- Size: 2.2 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# fastchaos
## About
`fastchaos` implement [integer chaos game representation (iCGR) algorithm](https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0173) for DNA sequence encoding and decoding. `fastchaos` is the first complete implementation of the algorithm in a bioinformatic tool aiming at users. It also add to the original algorithm a output file format which is a `zst` compressed JSON file containing the 3 integers of 100bp subsequences of the supplied sequence. This allow fast encoding and decoding.
`fastchaos` also implements [chaos game representation (CGR) of DNA sequence](https://academic.oup.com/nar/article-abstract/18/8/2163/2383530) in a fast tool that draw the representation of a sequence and can compare the CGR image using the [DSSIM algorithm](https://github.com/kornelski/dssim/).
## Installation
```bash
git clone https://github.com/Ebedthan/fastchaos.git
cd fastchaos
cargo build --release
```
## User guide
```bash
# Encoding DNA sequence into integer chaos game representation
fastchaos encode seq.fa
# Decoding integer chaos game representation into DNA sequence
fastchaos decode seq.icgr
# Draw chaos game representation of DNA sequence
fastchaos draw seq.fa
# Compare multiple chaos game representation image using DSSIM
fastchaos compare images_dir
```
For full details, do `fastchaos -h`.
### Requirements
- [Rust](https://rust-lang.org) in stable channel
### Minimum Rust version policy
This crate's minimum supported `rustc` version is `1.74.1`.
### Note
`fastchaos` use colored output in help, nevertheless `fastchaos` honors [NO_COLORS](https://no-color.org/) environment variable.
### Bugs
Submit problems or requests to the [Issue Tracker](https://github.com/Ebedthan/fastchaos/issues).
### License
Licensed under the MIT license ([LICENSE-MIT](LICENSE-MIT) or http://opensource.org/licenses/MIT).