Compression Algorithms for Genomic Data

Description

This project focuses on developing and comparing optimized compression algorithms for genomic data. The implemented algorithms, including Huffman Encoding and Run-Length Encoding (RLE), are designed to efficiently handle genomic sequences composed of nucleotide bases ('A', 'C', 'T', 'G'). This project aims to provide a robust tool for compressing genomic data, making it suitable for storage and analysis in the medical informatics and biotechnological field.

Required Technology

1. C++ Compiler

   • Any one of the following:
     • g++ (GNU C++ Compiler)
     • clang++ (LLVM C++ Compiler)
     • cl (MSVC Compiler for Windows)

2. CMake

   • Minimum version: 3.10

3. Build Tool

   • Any one of the following:
     • make
     • mingw32-make
     • ninja

4. Operating System-Specific Tools

   • Unix-like systems (Linux/Mac):
     • make or ninja
   • Windows:
     • mingw32-make or ninja
     • Ensure executables can run on the platform (.exe extensions).

5. Permissions for Installation

   • Write access to /usr/local/bin (on Unix-like systems) or an equivalent global binary directory.
   • Write access to the path details on Windows systems

Additional Notes

• PATH Configuration: If the script cannot copy the compressor executable to the installation directory (/usr/local/bin), you need to manually execute the provided command with sudo. If this is the case, the proper error message will appear.

• Testing Environment: Ensure the ./tests executable can run successfully after setup.

Setup

1. Clone this repository in and open in Visual Studio Code, navigating to the correct directory:

   git clone https://github.com/savinadd/Algorithms-for-Genomic-Compression
   cd Optimized-Algorithms-for-Genomic-Compression

2. Run the installation script in a terminal within Visual Studio Code

   ./install.sh

3. Successful setup is indicated by the following message at the end of the installation:

Setup complete! The project is ready to use.
To run the main program, use './compressor.exe' from the project root or 'compressor' if added to PATH.

If there is any missing technology on the computer attempting to run the compressor that is necessary, there will be a message detailing exactly what is missing and the installation script will exit. Please install all the necessary tools.

Usage

File formats

This tool supports only .txt files. However, it does support the use of .fasta files by way of a converter to a .txt file. To use it, run:

./clean_fasta.sh

You will be prompted to enter in the path to the file. The tool supports UNIX-style paths as well as Windows paths. The converted file will be written to a .txt in the root of the Optimized-Algorithms-for-Genomic-Compression folder. The output file name can be chosen or a default will be chosen. Here is an example:

MINGW64 ~/Desktop/Optimized-Algorithms-for-Genomic-Compression (main)
$ ./clean_fasta.sh
Enter the path to the input FASTA file: C:\Users\Savina\Downloads\sequence.fasta
Enter the path for the output file (default: cleaned_sequence.txt): example.txt
Cleaned sequence written to 'example.txt'

Using the Compressor

The compressor has a help menu. To access this help, run:

compressor -h orcompressor -help

It has the necessary information to get started with the compressor.

Example

In the data directory within the project, there are test data files. If we want to compress the file named datatest.txt and output the compressed file to a file called output.bin, for example, using the HuffmanGenome compressor version, we can run:

compressor -c -i data/datatest.txt -o output.bin -m huffmangenome

To decompress the file created by this and save the decompressed output to a file called output2.txt, we run:

compressor -d -i output.bin  -o output2.txt -m huffmangenome