Peptide SAR: MAFFT based API for multiple sequence alignment

API for the alignment of multiple peptide sequences represented in the HELM notation. Input sequences can contain up to 256 non-natural amino acids.

Deployment

1. Download and install MAFFT. Proceed to the MAFFT page. In the Download and Installation section choose your system and follow the installation instructions.

   By default MAFFT is installed into the /usr/local/bin/ folder. The same path for MAFFT is specified in the local.env file. Please, edit this file if you installed MAFFT into other folder.

2. Create Python 3.8 virtual environment and activate it:

   python3 -m venv ENV_NAME
   source ENV_NAME/bin/activate

3. Install dependencies specified in requirements.txt:

   python3 -m pip install -r requirements.txt

4. Run the API using uvicorn HTTP server. Execute the following command through the terminal, while you are in the root directory:

   uvicorn alignment.api:api --env-file local.env

5. Access the API through a web-browser. Copy the address specified on the last line of the terminal, after execution of the uvicorn command(by default it is http://127.0.0.1:8000), or you can use any API testing tool (e.g. Postman: https://www.postman.com/api-platform/)

Testing

Execute the following command to run all the tests:

python -m pytest -v

Execute the following command to run a specific test:

python -m pytest tests/unit_tests/*script_name* -v

Links

For more information about MAFFT follow this link https://mafft.cbrc.jp/alignment/software/

For more information on FastAPI deployment you can refer to: https://fastapi.tiangolo.com/deployment/

For more information on uvicorn package you can refer to: https://www.uvicorn.org/