Merge pull request #2 from uab-cgds-worthey/docker

Docker version

.dockerignore

@@ -0,0 +1,14 @@
+# .dockerignore
+**/__pycache__
+**/*.pyc
+**/*.pyo
+**/*.pyd
+*/*~
+.dockerignore
+.git
+.gitignore
+tests/
+*.log
+*.csv
+*.json
+*.md

Dockerfile

@@ -0,0 +1,22 @@
+# Use an official Python runtime as a parent image
+FROM python:3.11-slim-bookworm
+
+# Set environment variables
+ENV PYTHONDONTWRITEBYTECODE 1
+ENV PYTHONUNBUFFERED 1
+
+# Set work directory in the container
+WORKDIR /app
+
+# Install dependencies
+COPY requirements.txt /app/requirements.txt
+RUN pip install --no-cache-dir -r /app/requirements.txt
+
+# Copy the current directory contents into the container at /app
+COPY . /app/
+
+# Expose port
+EXPOSE 8000
+
+# Run the application:
+CMD ["uvicorn", "src.main:app", "--host", "0.0.0.0", "--port", "8000"]

README.md

@@ -14,43 +14,108 @@ Repo for querying DITTO predictions for variants using FastAPI.
 Following are required:
 
 - [git](https://git-scm.com/downloads)
-- python3.7+  & [python virtual environment](https://docs.python.org/3/tutorial/venv.html)
-- pip3
+- python3.7+
+- [Docker](https://www.docker.com/products/docker-desktop)
 
-## How to install
+## Installing
 
-Installation simply requires fetching the source code.
-
-To fetch source code, change in to directory of your choice and run:
+*1.* Clone the repository - change in to directory of your choice and run:
 
 ```sh
 git clone https://github.com/uab-cgds-worthey/DITTO-API.git
 ```
 
-Change in to root directory and run the command below to install environment:
+*2.* Navigate to the project directory
 
 ```sh
-# Create an environment. Needed only the first time.
-python3 -m venv ditto-api-env
-source ditto-api-env/bin/activate
-pip3 install -r requirements.txt
+cd DITTO-API
 ```
 
-## How to run
+*3.* Build the Docker image
+
+```sh
+docker build -t ditto-api .
+```
 
-Run the below command to activate the API
+*4.* Run the Docker container
 
 ```sh
-cd src
-uvicorn main:app --reload
+docker run -p 8000:8000 --name ditto-api ditto-api
 ```
 
-Test the app using this example as web address -
+*5.* Use this link in your browser to retrieve DITTO scores
+
 <!-- markdown-link-check-disable -->
 <http://localhost:8000/docs>
-<!-- markdown-link-check-enable -->
  and use this variant as example: 1-2406483-C-G
 
+## Expected result
+
+DITTO will output deleterious score by Ensemble transcript. Below is the output for the above test variant. To verify
+the scores, please query the variant in the [DITTO web app](https://cgds-ditto.streamlit.app/).
+<!-- markdown-link-check-enable -->
+
+```sh
+{
+  "scores_by_transcript": {
+    "ENST00000288774.7": {
+      "gene": "PEX10",
+      "consequence": "intron_variant,splice_site_variant",
+      "chrom": "chr1",
+      "pos": "2406483",
+      "ref_base": "C",
+      "alt_base": "G",
+      "DITTO": "1.0"
+    },
+    "ENST00000447513.6": {
+      "gene": "PEX10",
+      "consequence": "intron_variant,splice_site_variant",
+      "chrom": "chr1",
+      "pos": "2406483",
+      "ref_base": "C",
+      "alt_base": "G",
+      "DITTO": "1.0"
+    },
+    "ENST00000507596.5": {
+      "gene": "PEX10",
+      "consequence": "intron_variant,splice_site_variant",
+      "chrom": "chr1",
+      "pos": "2406483",
+      "ref_base": "C",
+      "alt_base": "G",
+      "DITTO": "1.0"
+    },
+    "ENST00000510434.1": {
+      "gene": "PEX10",
+      "consequence": "2kb_downstream_variant,NMD_transcript_variant",
+      "chrom": "chr1",
+      "pos": "2406483",
+      "ref_base": "C",
+      "alt_base": "G",
+      "DITTO": "1.0"
+    },
+    "ENST00000378513.7": {
+      "gene": "RER1",
+      "consequence": "2kb_downstream_variant",
+      "chrom": "chr1",
+      "pos": "2406483",
+      "ref_base": "C",
+      "alt_base": "G",
+      "DITTO": "1.0"
+    },
+    "ENST00000605895.6": {
+      "gene": "RER1",
+      "consequence": "2kb_downstream_variant",
+      "chrom": "chr1",
+      "pos": "2406483",
+      "ref_base": "C",
+      "alt_base": "G",
+      "DITTO": "1.0"
+    }
+  }
+}
+```
+
 ## Contributing
 
 We welcome contributions! [See the docs for guidelines](./CONTRIBUTING.md).
@@ -60,6 +125,6 @@ We welcome contributions! [See the docs for guidelines](./CONTRIBUTING.md).
 For issues, please send an email with clear description to
 
 |Name | Email |
-------|--------|
-Tarun Mamidi | <[email protected]>
-Brandon Wilk | <[email protected]>
+|------|--------|
+|Tarun Mamidi | <[email protected]>|
+|Brandon Wilk | <[email protected]>|

src/main.py

@@ -1,6 +1,5 @@
 from fastapi import FastAPI
-from utils.query import get_ditto_score, query_variant
-import json
+from .utils.query import get_ditto_score, query_variant
 
 #  run me https://fastapi.tiangolo.com/#installation
 app = FastAPI()

src/utils/query.py

@@ -1,8 +1,8 @@
 import yaml
 import requests
 import json
-from utils.parse import OCApiParser
-from utils.predict import parse_and_predict
+from .parse import OCApiParser
+from .predict import parse_and_predict
 from tensorflow import keras
 from pathlib import Path