112 lines
2.4 KiB
Markdown
112 lines
2.4 KiB
Markdown
# locimend
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locimend is a tool that corrects DNA sequencing errors using Deep Learning.
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The goal is to provide a correct DNA sequence, when a sequence containing errors is provided.
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It provides both a command-line program and a REST API.
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## Technologies
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- Tensorflow
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- Biopython
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- FastAPI
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## Installation
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This project uses [Nix](https://nixos.org/) to ensure reproducible
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builds.
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1. Install Nix (compatible with MacOS, Linux and
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[WSL](https://docs.microsoft.com/en-us/windows/wsl/about)):
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```bash
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curl -L https://nixos.org/nix/install | sh
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```
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2. Clone the repository:
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```bash
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git clone https://git.coolneng.duckdns.org/coolneng/locimend
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```
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3. Change the working directory to the project:
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```bash
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cd locimend
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```
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4. Enter the nix-shell:
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```bash
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nix-shell
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```
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5. Install the dependencies via poetry:
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```bash
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poetry install
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```
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After running these commands, you will find yourself in a shell that
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contains all the needed dependencies.
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## Usage
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### Training the model
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The following command creates the trains the Deep Learning model and shows the accuracy and AUC:
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```bash
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poetry run python locimend/main.py train <data file> <label file>
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```
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- <data file>: FASTQ file containing the sequences with errors
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- <label file>: FASTQ file containing the sequences without errors
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Both files must contain the canonical and read simulated sequences in the same positions (same row).
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A dataset is provided to train the model, in order to proceed execute the following command:
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```bash
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poetry run python locimend/main.py train data/curesim-HVR.fastq data/HVR.fastq
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```
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### Inference
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A trained model is provided, which can be used to infer the correct sequences. There are two ways to interact with it:
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- Command-line execution
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- REST API
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#### Command-line
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The following command will infer the correct sequence, and print it:
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```bash
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poetry run python locimend/main.py infer "<DNA sequence>"
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```
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#### REST API
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It is also possible to serve the model via a REST API, to start the web server run the following command:
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```bash
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poetry run api
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```
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The API can be accessed at http://localhost:8000, with either a GET or POST request:
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| Request | Endpoint | Payload |
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|:----:|:-----:|:-----:|
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| GET | / | Sequence as a path parameter (in the URL) |
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| POST | /| JSON |
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For a POST request the JSON must have the following structure:
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```json
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{"sequence": "<DNA sequence>"}
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```
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