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Marco Lenoir
MarcoTheBlack/
DNAnalyzer
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Welcome to the DNAnalyzer Wiki!

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

Contributing

Steps to follow 📜

  1. Fork it 🍴
    Get your own fork of DNAnalyzer by using the Fork button at the top right of this page.

  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 and 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:

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

or

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

To view the help message:

<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

Samples