jacobfh1 / fasta-parser

The FASTA Parser Script is a Python tool for analyzing DNA or protein sequences, providing sequence statistics and generating tab-separated values (TSV) output files.

FASTA Parser

This script is designed to perform sequence analysis on FASTA files. It calculates sequence statistics, generates a TSV output file, and provides various functionalities for analyzing protein sequences.

Features

• Parsing FASTA files to extract sequence data
• Calculating sequence statistics such as total sequences, average length, minimum length, and maximum length
• Saving the analysis results to a tab-separated values (TSV) file
• Identifying sequences with minimum and maximum lengths
• Optional protein domain analysis using InterProScan or Pfam (not implemented)
• Customizable alignment parameters for protein sequences (not implemented)
• Comparison of sequences using pairwise alignment (not implemented)

Dependencies

The following dependencies are required to run the script:

• Python 3.x
• Biopython

Install the dependencies using the following command:

pip install biopython

Usage

1. Ensure you have Python 3.x installed on your system.

2. Install the required dependencies using the command mentioned above.

3. Prepare a FASTA file containing the input sequences.

4. Update the input_file and output_file variables in the script with the appropriate file paths.

5. Run the script using the following command:

   python fasta_parser.py
   

6. The output will be saved in the specified output file as a TSV format, containing the sequence names, lengths, and sequences themselves.

7. You can modify the script parameters and alignment settings as needed for your specific analysis by editing the fasta_parser.py file.

Contributing

Contributions to the project are welcome! If you have any suggestions, bug reports, or feature requests, please open an issue or submit a pull request.

License

This project is licensed under the MIT License.