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https://github.com/Merck/PepSeA
https://github.com/Merck/PepSeA
Last synced: 13 days ago
JSON representation
- Host: GitHub
- URL: https://github.com/Merck/PepSeA
- Owner: Merck
- License: mit
- Created: 2021-10-27T20:19:41.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2021-10-27T20:27:01.000Z (over 3 years ago)
- Last Synced: 2025-01-09T02:11:31.314Z (23 days ago)
- Language: Python
- Size: 6.35 MB
- Stars: 22
- Watchers: 6
- Forks: 9
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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- top-pharma50 - **Merck/PepSeA** - 10-27 20:27:01 | (Ranked by starred repositories)
README
# Peptide SAR: MAFFT based API for multiple sequence alignment
API for the alignment of multiple peptide sequences represented in the [HELM notation](https://www.pistoiaalliance.org/helm-notation/). Input sequences can contain up to 256 non-natural amino acids.
## Deployment
1) Download and install MAFFT. Proceed to the MAFFT [page](https://mafft.cbrc.jp/alignment/software/). 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:
```bash
python3 -m venv ENV_NAME
source ENV_NAME/bin/activate
```
3) Install dependencies specified in __requirements.txt__:
```bash
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:
```bash
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/