Syn_Tool

Syn_Tool is a deep learning framework designed for analyzing Synechococcus ITS sequences. It integrates identification, classification, and novel clade delineation into a single streamlined workflow. With minimal setup, you can process sequence data and abundance information to gain insights into Synechococcus communities.

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Installation

Requirements

• Python Version: Python 3.8 or later
• Dependencies: Listed in requirements.txt

Steps

1. Clone the repository:

   git clone https://github.com/Aldred-Wang/Syn_Tool.git
   cd Syn_Tool

2. Install dependencies:

   pip install -r requirements.txt

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Usage

Before running the tool, ensure that the following files are placed inside the model folder:

• Syn_Tool_run.py
• input_sequences.fasta
• input_abundance.txt

Run the following command to start the tool:

python Syn_Tool_run.py -fa input_sequences.fasta -a input_abundance.txt

Parameters

• -fa or --fasta: Path to the input FASTA file.
• -a or --abundance: Path to the abundance file.

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Example

Here’s an example of how to use Syn_Tool:

python Syn_Tool_run.py -fa example_sequences.fasta -a example_abundance.txt

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Output

After execution, the following files will be generated:

• Syn.fasta: Output file from the identification module containing Synechococcus ITS sequences in FASTA format.
• Syn_df.csv: Output file from the identification module containing Synechococcus ITS sequences in CSV format.
• combined_df.csv: Output file from the classification module containing feature vectors of Synechococcus ITS sequences extracted by the CNN model.
• result.csv: Output file from the novel clade delineation module providing information about Synechococcus novel clades.
• Syn_Tool_final_result.txt: Final classification file generated by Syn_Tool.

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Citation

If you use Syn_Tool in your research, please cite:

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Contact

For questions or issues, please contact:

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