From 2ea80006575af935f950e37a789a6e18ed8940b3 Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Wed, 7 Jul 2021 00:05:12 +0200
Subject: [PATCH] Update README

---
 README.md | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 58 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 3bc8bdc..9031f3e 100644
--- a/README.md
+++ b/README.md
@@ -2,10 +2,15 @@
 
 locimend is a tool that corrects DNA sequencing errors using Deep Learning.
 
+The goal is to provide a correct DNA sequence, when a sequence containing errors is provided.
+
+It provides both a command-line program and a REST API.
+
 ## Technologies
 
 - Tensorflow
 - Biopython
+- FastAPI
 
 ## Installation
 
@@ -48,8 +53,59 @@ contains all the needed dependencies.
 
 ## Usage
 
-The following command creates the dataset, trains the Deep Learning model and shows the accuracy:
+### Training the model
+
+The following command creates the trains the Deep Learning model and shows the accuracy and AUC:
 
 ```bash
-poetry run python src/model.py
+poetry run python locimend/main.py train <data file> <label file>
 ```
+
+- <data file>: FASTQ file containing the sequences with errors
+- <label file>: FASTQ file containing the sequences without errors
+
+Both files must contain the canonical and read simulated sequences in the same positions (same row).
+
+A dataset is provided to train the model, in order to proceed execute the following command:
+
+```bash
+poetry run python locimend/main.py train data/curesim-HVR.fastq data/HVR.fastq
+```
+
+
+### Inference
+
+A trained model is provided, which can be used to infer the correct sequences. There are two ways to interact with it:
+
+- Command-line execution
+- REST API
+
+#### Command-line
+
+The following command will infer the correct sequence, and print it:
+
+```bash
+poetry run python locimend/main.py infer "<DNA sequence>"
+```
+
+#### REST API
+
+It is also possible to serve the model via a REST API, to start the web server run the following command:
+
+```bash
+poetry run api
+```
+
+The API can be accessed at http://localhost:8000, with either a GET or POST request:
+
+| Request | Endpoint | Payload |
+|:----:|:-----:|:-----:|
+| GET     | / | Sequence as a path parameter (in the URL) |
+| POST     | /| JSON |
+
+For a POST request the JSON must have the following structure:
+
+```json
+{"sequence": "<DNA sequence>"}
+```
+