CDSMatch

Overview

CDSMatch is a Python package and command-line tool designed for matching IDs from two different genome annotation sources based on sequence similarity. It is particularly useful for tasks such as:

• Data reconciliation
• Entity resolution
• Fuzzy matching of genomic annotations

By leveraging sequence similarity, this tool enables researchers and bioinformaticians to map genome annotation identifiers across different datasets with high accuracy.

Features

• Sequence-based ID matching: Uses sequence similarity to align genome annotation IDs.
• Command-line utility: Easily executable from the terminal for automated workflows.
• Python API: Can be integrated into custom scripts and pipelines.
• Efficient processing: Optimized for handling large-scale genomic datasets.

Installation

git clone https://github.com/zitunstu24/CDSMatch.git
cd CDSMatch
pip install .

Usage

Command-Line Interface (CLI)

CDSMatch --config config.yml

Parameters

Parameter	Description
--config	Path to the config file (yml format)

Configuration

This tool uses a YAML file for configuration. You can customize various aspects, such as directories for genomes, output locations, and STAR parameters.

An example configuration file can be found at config/config.yml. Here's a typical structure:

cds_file_X: "data/input/NCBI_lotus_cds.fa"
cds_file_Y: "data/input/lotus_cds.fa"
blast_db: "data/output/ncbi_cds_db"
XML_output: "data/output/results.xml"
output_dir: "data/output"
output_csv: "CDSMatch_results.csv"
evalue: 0.001

Dependencies

• Python 3.7+
• Biopython
• Pandas
• NumPy
• ace_tools_open

Contributing

We welcome contributions! Feel free to submit issues, feature requests, or pull requests on our GitHub repository.

Contact

For questions or support, please reach out via the GitHub issues or email me at abul.khayer@mpimp-golm.mpg.de or zitunstu24@gmail.com.