ResTransfer v1.0.0 Release

Release Name: ResTransfer v1.0.0 - Initial Stable Release
Release Date: 24-December-2024

Features
Horizontal Gene Transfer Prediction:

Predicts the likelihood of resistance gene transfer (HGT) in microbial genomes.
Supports BLAST-based identification of gene categories: Resistance, T4SS, ICE, and Adherence.
Gene Categorization:

Automated categorization of genes based on predefined categories with scoring for each.
Scoring System:

Assigns weighted scores to gene categories for assessing resistance transfer likelihood.
Classifies results into three categories:
High chance for antibiotic resistance gene transfer.
Moderate chance for antibiotic resistance gene transfer.
Low chance for antibiotic resistance gene transfer.
Machine Learning Integration:

Placeholder for Random Forest model for advanced predictions (planned in the next release).
Excel Output:

Outputs detailed results, including total scores and HGT likelihood, in an easy-to-read Excel format.
Installation
Refer to the README.md for detailed installation instructions.

Usage
Prepare input files:

Query genome in FASTA format.
Reference database for BLAST.
Run the pipeline:

bash
Copy code
python ResTransfer.py
View the output in Gene_Counts.xlsx.

System Requirements
Python: Version 3.8 or higher.
Dependencies:
pandas
openpyxl
BLAST+: Installed and configured on your system.
Changelog
Added BLAST-based HGT prediction.
Introduced scoring system for gene categories.
Enabled Excel output for results.
Automated categorization for Resistance, T4SS, ICE, and Adherence genes.
Known Issues
Random Forest model integration is planned for the next release.
Limited to microbial genomic datasets compatible with BLAST.
Future Plans
Add support for protein-level BLAST (blastp) and other alignment tools.
Integrate advanced machine learning models for dynamic predictions.
Extend support for additional microbial families.
Contributors
Umeshkumar KU - Primary Developer and Maintainer
License
This project is licensed under the Apache License, Version 2.0. See the LICENSE file for details.