{"id":20690244,"url":"https://github.com/merck/pepsea","last_synced_at":"2025-04-22T16:56:19.600Z","repository":{"id":90243151,"uuid":"421962143","full_name":"Merck/PepSeA","owner":"Merck","description":null,"archived":false,"fork":false,"pushed_at":"2021-10-27T20:27:01.000Z","size":6659,"stargazers_count":24,"open_issues_count":3,"forks_count":9,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-03-29T16:51:14.399Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Merck.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2021-10-27T20:19:41.000Z","updated_at":"2025-01-31T17:24:46.000Z","dependencies_parsed_at":"2023-03-17T21:00:24.631Z","dependency_job_id":null,"html_url":"https://github.com/Merck/PepSeA","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Merck%2FPepSeA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Merck%2FPepSeA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Merck%2FPepSeA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Merck%2FPepSeA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Merck","download_url":"https://codeload.github.com/Merck/PepSeA/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250284110,"owners_count":21405288,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-16T23:12:23.090Z","updated_at":"2025-04-22T16:56:19.578Z","avatar_url":"https://github.com/Merck.png","language":"Python","readme":"# Peptide SAR: MAFFT based API for multiple sequence alignment\n\nAPI 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.\n\n## Deployment\n\n1) 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. \n\n    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.\n\n2) Create Python 3.8 virtual environment and activate it:\n    ```bash\n    python3 -m venv ENV_NAME\n    source ENV_NAME/bin/activate\n    ```\n\n3) Install dependencies specified in __requirements.txt__:\n    ```bash\n    python3 -m pip install -r requirements.txt\n    ```\n   \n4) Run the API using uvicorn HTTP server. Execute the following command through the terminal, while you are in the root directory:\n    ```bash\n    uvicorn alignment.api:api --env-file local.env\n    ```\n   \n5) 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/)\n\n\n## Testing\nExecute the following command to run all the tests:\n\n    python -m pytest -v\n    \nExecute the following command to run a specific test:\n\n    python -m pytest tests/unit_tests/*script_name* -v\n\n## Links    \nFor more information about MAFFT follow this link https://mafft.cbrc.jp/alignment/software/\n \nFor more information on FastAPI deployment you can refer to: https://fastapi.tiangolo.com/deployment/\n  \nFor more information on uvicorn package you can refer to: https://www.uvicorn.org/\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmerck%2Fpepsea","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmerck%2Fpepsea","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmerck%2Fpepsea/lists"}