Welcome to pyaragorn! This repository provides Cython bindings and a Python interface to ARAGORN, a powerful tool for identifying (t|mt|tm)RNA genes. With this library, you can easily integrate RNA gene-finding capabilities into your Python projects.
In the field of bioinformatics, identifying RNA genes is crucial for understanding the genome's functionality. pyaragorn simplifies this process by providing a straightforward interface to ARAGORN, which is designed to locate tRNA and mtRNA genes efficiently. Whether you are a researcher or a developer, this library can enhance your projects by streamlining RNA gene identification.
- Cython Bindings: Leverage the speed of Cython for performance-critical applications.
- Easy Integration: Use the library directly in your Python projects with minimal setup.
- Comprehensive Documentation: Access detailed guides and examples to get started quickly.
- Support for Multiple RNA Types: Identify tRNA, mtRNA, and tmRNA genes seamlessly.
To install pyaragorn, follow these steps:
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Ensure you have Python installed. You can download it from python.org.
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Clone the repository:
git clone https://github.com/darkranger22/pyaragorn.git cd pyaragorn -
Install the required dependencies:
pip install -r requirements.txt
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Build the Cython bindings:
python setup.py build_ext --inplace
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Optionally, you can download the latest release from the Releases page. Download the appropriate file, then execute it to set up the library.
Here's a quick example to get you started with pyaragorn:
from pyaragorn import Aragorn
# Initialize the ARAGORN object
aragorn = Aragorn()
# Load your genomic sequence
sequence = "ATGCGTAGCTAGCTAGCTAGCTAGCTAGCTAGCTAGC"
# Find RNA genes
results = aragorn.find_genes(sequence)
# Print the results
for gene in results:
print(f"Found gene: {gene}")This code snippet initializes the ARAGORN object, loads a genomic sequence, and prints out the identified RNA genes. You can expand this example to include more advanced features and options available in the library.
We welcome contributions to pyaragorn! If you would like to contribute, please follow these steps:
- Fork the repository.
- Create a new branch for your feature or bug fix.
- Make your changes and commit them.
- Push your branch to your fork.
- Open a pull request.
Please ensure that your code adheres to the project's coding standards and includes appropriate tests.
This project is licensed under the MIT License. See the LICENSE file for details.
- ARAGORN: The original software that inspired this library.
- Cython: For providing a powerful way to write C extensions for Python.
- The bioinformatics community for their ongoing contributions and support.
For more details, visit the Releases section to download the latest version or check for updates.
Happy coding! 🧬