kmertools: DNA Vectorisation Tool (Fork with New KML Function)

$$\   $$\                                   $$$$$$$$\                     $$\           
$$ | $$  |                                  \__$$  __|                    $$ |          
$$ |$$  / $$$$$$\$$$$\   $$$$$$\   $$$$$$\     $$ |    $$$$$$\   $$$$$$\  $$ | $$$$$$$\ 
$$$$$  /  $$  _$$  _$$\ $$  __$$\ $$  __$$\    $$ |   $$  __$$\ $$  __$$\ $$ |$$  _____|
$$  $$<   $$ / $$ / $$ |$$$$$$$$ |$$ |  \__|   $$ |   $$ /  $$ |$$ /  $$ |$$ |\$$$$$$\  
$$ |\$$\  $$ | $$ | $$ |$$   ____|$$ |         $$ |   $$ |  $$ |$$ |  $$ |$$ | \____$$\ 
$$ | \$$\ $$ | $$ | $$ |\$$$$$$$\ $$ |         $$ |   \$$$$$$  |\$$$$$$  |$$ |$$$$$$$  |
\__|  \__|\__| \__| \__| \_______|\__|         \__|    \______/  \______/ \__|\_______/ 

Overview

This repository is a fork of the original Kmertools project that adds a new function: KML.
The KML function generates a table from DNA vectorisation data, streamlining the creation of datasets ready for machine learning applications. All other original features of Kmertools remain intact, including:

• Oligonucleotide Frequency Vectors: Generate frequency vectors for oligonucleotides.
• Minimiser Binning: Efficiently bin sequences using minimisers to reduce data complexity.
• Chaos Game Representation (CGR): Compute CGR vectors for DNA sequences using k-mers or full sequence transformation.
• Coverage Histograms: Create coverage histograms to analyze sequencing read depth.
• Python Binding: Import kmertools functionality using import pykmertools as kt.

Installation from Sources

To install kmertools (including the new KML functionality) from source, follow these steps. Make sure you have Rust and its package manager cargo installed.

# Clone the repository
git clone https://github.com/aaguirreu/kmertools4ml.git
cd kmertools

# Build the project in release mode
cargo build --release

Add the generated binary to your PATH (you can modify your ~/.bashrc or ~/.zshrc):

# To add it to the current terminal session:
export PATH=$PATH:$(pwd)/target/release/

# To add it permanently (for Bash):
echo "export PATH=\$PATH:$(pwd)/target/release/" >> ~/.bashrc
source ~/.bashrc

# For Zsh (e.g., on macOS):
echo "export PATH=\$PATH:$(pwd)/target/release/" >> ~/.zshrc
source ~/.zshrc

Testing the Installation

After installation, verify everything is set up correctly by running:

kmertools --help

This command should display the help message, confirming that the program (including the new KML functionality) is working as expected.