Quadruplex generator

Quadruplex generator is python script used to generate artificial guanine quadruplex sequences.

Requirements

Quadruplex generator was built with Python 3.7+.

Installation

To run quadruplex generator run

poetry install

Generate G-quadruplexes

To generate G-quadruplexes withou artificial noise run.

if __name__ == "__main__":
    generator = QuadruplexGenerator()
    generator.run(limit_per_regex=10)

    print(generator.quadruplexes)

If artificial noise is needed run

if __name__ == "__main__":
    generator = QuadruplexGenerator()
    generator.run(
        limit_per_regex=10,
        place_random_noise=True,
        minimum_number_of_noise=1,
        maximum_number_of_noise=3,
    )

    print(generator.quadruplexes)

All generated quadruplexes are stored in class variable quadruplexes.

print(generator.quadruplexes)

> [
    'GGGGGAGAGTGCCGGGGGATAACGGG', 
    'GGGACCAACAGGGGCGGGATACTTGGGG', 
    'GAGGAGGGGCACCAGGGGGTTCCAAAGGGGG', 
    'GGTGCGGGTTAGGGGCATTTAGGGG',
    ...
  ]

Dependencies

• exrex = "^0.10.5"

Authors

• Patrik Kaura - Main developer - patrikkaura

License

This project is licensed under the MIT License - see the LICENSE file for details.