fastchaos implement integer chaos game representation (iCGR) algorithm 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 in a fast tool that draw the representation of a sequence and can compare the CGR image using the DSSIM algorithm.
git clone https://github.com/Ebedthan/fastchaos.git
cd fastchaos
cargo build --release# 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_dirFor full details, do fastchaos -h.
- Rust in stable channel
This crate's minimum supported rustc version is 1.74.1.
fastchaos use colored output in help, nevertheless fastchaos honors NO_COLORS environment variable.
Submit problems or requests to the Issue Tracker.
Licensed under the MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT).