edited for publication

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+mlruns/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+# Usually these files are written by a python script from a template
+# before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+logs/
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+# However, in case of collaboration, if having platform-specific dependencies or dependencies
+# having no cross-platform support, pipenv may install dependencies that don't work, or not
+# install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

README.md

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+# Confirmed Variant Recommendation System (ASC3)
+Disease similarity (22-3Q-OKR13) 
+: API to calcualting disease similarity to server GEBRA webpage using TCP socket (https://gebra.io). API requires three data modal including ACMG baysian score, semantic simiarity based on HPO ontology, and etc With these scores, model based on linear regression return disesase similartiy score. 
+
+
+## Contents
+- `/ASC3`: 변이추천시스템의 구동 폴더
+- `/ASC3/__main__.py`: ASC3 폴더를 동작시기 위한 최상위 코드 (app.py을 구동)
+- `/ASC3/app.py`: FastAPI을 동작시키는 메인 모듈
+- `/ASC3/models.py`: 쿼리 변이들과 변이들의 특징값을 인자로하여 컨펌 변이의 확률을 추론하는 추론기
+- `/ASC3/utils.py`: 로깅과 YAML파일을 로딩하는 유틸
+- `/ASC3/logs`: 로그 폴더
+- `/validation`: Validation 샘플과 모델 서치를 하기 위한 폴더
+- `/anaylsis_code`: 통계량 분석을 위한 ipynb을 담고 있는 폴더
+```
+.
+├── ASC3
+│ ├── __main__.py
+│ ├── app.py
+│ ├── models.py
+│ ├── config.yaml
+│ ├── routers.py
+│ ├── utils.py
+│ ├── logs
+│ └── tests
+├── anaylsis_code
+├── backup
+├── data
+│ └── validation_samples
+├── README.md
+├── requirements.txt
+└── validation
+ ├── config.yaml
+ ├── mlruns
+ ├── model_search_with_mlflow.py
+ ├── tests
+ ├── validation_samples_generator.py
+ ├── validation_utils.py
+ └── validator.py
+```
+
+
+## Requirement
+1. PyYAML
+2. locust
+3. Python3.7 ~
+4. sklearn >= 0.24.2
+
+## Install
+TODO
+
+
+## How to use?
+For server (Linux)
+```
+$ python3 ASC3
+```
+
+For client
+```
+curl -X 'POST' \
+ 'https://127.0.0.1:8000/predict' \
+ -H 'accept: application/json' \
+ -H 'Content-Type: application/json' \
+ -d '{
+ "sample_id": "TEST_SAMPLE",
+ "inhouse_total_ac": 100,
+ "gene_diseases": {
+ "OMIM:600276-OMIM:125310": {
+ "1-100-A-T": {
+ "acmg_bayesian": 1,
+ "qual": 1271.77,
+ "ad": "287.27",
+ "dp": 129.0,
+ "disease_similarity": 3.09534946,
+ "inhouse_variant_ac": 237
+ },
+ "1-200-A-T": {
+ "acmg_bayesian": 0.99409,
+ "qual": 1271.77,
+ "ad": "287.27",
+ "dp": 129.0,
+ "disease_similarity": 5.09534946,
+ "inhouse_variant_ac": 3
+ }
+ },
+ "OMIM:12367-OMIM:23223": {
+ "3-100-A-T": {
+ "acmg_bayesian": 0.99409,
+ "qual": 1271.77,
+ "ad": "287.27",
+ "dp": 129.0,
+ "disease_similarity": -1.09534946,
+ "inhouse_variant_ac": 237
+ },
+ "3-200-A-T": {
+ "acmg_bayesian": 0.99409,
+ "qual": 1271.77,
+ "ad": "287.27",
+ "dp": 129.0,
+ "disease_similarity": -1.09534946,
+ "inhouse_variant_ac": 237
+ }
+ }
+ }
+}
+'
+```
+
+
+## Credit
+- Heon
+- Isaac
+- Tyler
+- Kyle 
+
+Reviwed by seom, jame
+
+
+## License
+todo