# Welcome to the DNAnalyzer Wiki!

![](https://user-images.githubusercontent.com/96280466/186224441-46dd2029-b9dc-4b3d-aad8-bfd1e1e62f2e.png)

> DNAnalyzer identifies proteins, amino acids, start and stop codons, high coverage regions, and regulatory elements.

> Researchers are working to extract valuable information to better understand human health and disease.

> Currently, we are developing a Command-Line Interface (CLI) and a Graphical User Interface (GUI) to enable physicians

> to quickly identify genetic mutations.

## Documents

[View Documents](https://github.com/VerisimilitudeX/DNAnalyzer/tree/main/docs)

## Contributing

### Steps to follow 📜

1. **Fork it 🍴**  

   Get your own fork of [DNAnalyzer](https://github.com/VerisimilitudeX/DNAnalyzer) by using the `Fork` button at the top right of this page.  

   ![](https://github-images.s3.amazonaws.com/help/bootcamp/Bootcamp-Fork.png)

2. **Clone it 👥**  

   Clone your fork to your local machine:

   ```bash

   git clone https://github.com/Your_Username/DNAnalyzer.git

   cd DNAnalyzer

   ```

   Then, add a reference to the original repository:

   ```bash

   git remote add upstream https://github.com/theabhishek07/DNAnalyzer.git

   git remote -v

   ```

3. **Sync with the Remote 🔄**  

   Keep your local repository up-to-date:

   ```bash

   git fetch --all --prune

   git checkout main

   git reset --hard upstream/main

   git push origin main

   ```

4. **Create a new branch**  

   Create a new branch for your contribution:

   ```bash

   git checkout -b <branchname>

   ```

   To switch branches later:

   ```bash

   git checkout <branchname>

   ```

   Add changes and commit:

   ```bash

   git add .

   git commit -m "your commit message"

   ```

   Push your branch:

   ```bash

   git push -u origin <branchname>

   ```

   Finally, in your browser, navigate to your repository, click **Contribute**, and then **Open Pull Request**. Provide a concise title and description describing your contribution.

### Contribution Guideline

- ⭐ Drop a star on the GitHub repository (optional).

- Before contributing, please read [`Contributing_Guidelines.md`](Contributing_Guidelines.md) and [`CODE_OF_CONDUCT.md`](CODE_OF_CONDUCT.md).

- Create an issue or propose a feature/bug fix.

- Fork the repo, clone it, create a branch, add your changes, commit, and push.

- Make a pull request comparing your branch with the main branch of the repository.

## Usage

### Command-Line Interface (CLI) Usage

DNAnalyzer uses CLI arguments instead of standard input. For example:

```bash

<executable> assets/dna/random/dnalong.fa --amino=ser

```

or

```bash

<executable> assets/dna/random/dnalong.fa --amino=ser --min=0 --max=100

```

To view the help message:

```bash

<executable> --help

# Output:

Usage: DNAnalyzer [-hrV] --amino=<aminoAcid> [--find=<proteinFile>] [--max=<maxCount>] [--min=<minCount>] DNA

  DNA                    The FASTA file to be analyzed.

  --amino=<aminoAcid>    The amino acid representing the start of a gene.

  --find=<proteinFile>   The DNA sequence to be found.

  -h, --help             Show this help message and exit.

  --max=<maxCount>       Maximum count of the reading frame.

  --min=<minCount>       Minimum count of the reading frame.

  -r, --reverse          Reverse the DNA sequence before processing.

  -V, --version          Print version information and exit.

```

## Reports

- [Key Personnel and Knowledge Distribution](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/key-personnel-and-and-knowledge-distribution.pdf)

- [Technical Health Overview](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/technical-health-overview.pdf)

- [Trend Report](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/reports/trend-report.pdf)

## Samples

- [Serine DNAlong](https://github.com/VerisimilitudeX/DNAnalyzer/blob/936181dd714855276ea34f55b94e5b53afc8ef0e/docs/samples/serine-dnalong.md)