idptools-hoatzin 0.12

A Python package for DNA-based evolution of protien sequences. Holistic apprOach for SequAnces To underZtand evolutIoN.

hoatzin

A Python package for DNA-based evolution of protien sequences. Holistic apprOach for SequAnces To underZtand evolutIoN.

Last updated August 2023

Current version: v0.12

Installation

The current stable version of hoatzin is available through GitHub or the Python Package Index (PyPI).

To install from PyPI, run:

pip install idptools-hoatzin

You can also install the current development version from

pip install git+https://[e-mail]/idptools/hoatzin

To clone the GitHub repository and gain the ability to modify a local copy of the code, run

git clone https://github.com/idptools/hoatzin.git
cd hoatzin
pip install -e .

Usage

First import hoatzin

from hoatzin import evolve

Evolving Sequences

The evolve.sequence() function lets you evolve protein or DNA sequences. If you input a protein sequence, it will be turned into a DNA sequence using the codon usage frequencies from humans. The probabilities for each mutation then use nucleotide mutation probabilities that are from COSMIC 2023, which examined the frequencies of non-synonymous mutations in the human genome. The evolve.sequence() function requires that you input a sequence as the first argument and then the number of generations as the second argument. 1 DNA mutation per generation is assumed.

sequence='QQQGSRGSGSGRRRGSGSGQGS'
evolved_sequence = evolve.sequence(sequence, number_generations=10)
print(evolved_sequence)

Which would return something like:

QQQGPSGSRNGRRRGFSGGLDS

Optional Arguments:

Using the evolve.sequence() function, you can specify additional parameters. mutations_per_generation - the number of DNA mutations in each 'mutation' generation. mutation_probs - The probabilities of each mutation. You can specify your own dictionary of mutations. See NUCLEOTIDE_MUTATION_PROBS in hoatzin_parameters to specify this. sequence_type - Lets you specify if you want to mutate a DNA sequence or a protein sequence. You must specify as 'nucleotide_sequence' if you are inputting a nucleotide sequence. codon_probs - Lets you specify the probabilities of each codon when going from a protein sequence to a DNA sequence. return_all_seqs - Lets you specify whether to return all sequences generated (one sequence per generation) or just get back a single final sequence.

Example

sequence='QQQGSRGSGSGRRRGSGSGQGS'
evolved_sequence = evolve.sequence(sequence, number_generations=10, return_all_seqs=True)
print(evolved_sequence)

Would return something like...

{'original': 'QQQGSRGSGSGRRRGSGSGQGS', 1: 'QQQGSRGSGSGHRRGSGSGQGS', 2: 'QQQGSRGSGSGHRRGSGSGQGS', 3: 'QQQGSRGSGSGHKRGSGSGQGS', 4: 'QQQGSRGSGSGDKRGSGSGQGS', 5: 'QRQGSRGSGSGDKRGSGSGQGS', 6: 'QRQGSRGSGSGDKRGSGSGQGL', 7: 'QRQGSRGFGSGDKRGSGSGQGL', 8: 'QRQGSRGFRSGDKRGSGSGQGL', 9: 'QREGSRGFRSGDKRGSGSGQGL', 10: 'QREG*RGFRSGDKRGSGSGQGL'}

Copyright

Copyright (c) 2023, Ryan Emenecker - Holehouse Lab

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.1.