omatheuspimenta/seq_generatoRS

This tool allows users to simulate DNA sequences with mutations, variations, and bias. Ideal for quick experiments, testing, or academic purposes, it provides a simple yet powerful solution for generating synthetic DNA data in the Rust programming language.

seq_generatoRS

seq_generatoR is a random DNA sequence generator written in Rust.

Install

To install seq_generatoRS, run the following commands:

git clone git@github.com:omatheuspimenta/seq_generatoRS.git
cd seq_generatoRS
cargo install --path . 

Tests and Docs

Generate tests and documentation with the following commands:

cargo doc
cargo test

Usage

seq_generatoRS functions as a command-line interface (CLI).

help

seq_generator --help
Generate randon DNA sequences with mutations, variations and bias.

Usage: seq_generator [OPTIONS]

Options:
      --records-number <RECORDS_NUMBER>
          Number of records to be generated [default: 1000]
      --records-length <RECORDS_LENGTH>
          Length of each record [default: 10000]
      --mutation-rate <MUTATION_RATE>
          Mutation rate Rates of evolutionary change in viruses: patterns and determinants Another relationship between mutation rate and genome size was noted by Drake, who proposed a 'universal' genomic mutation rate in DNA microorganisms of 3.4*10^–3 mutations per genome, per genomic replication. [REFERENCE](https://www.nature.com/articles/nrg2323) [default: 0.0034]
      --bias-rate <BIAS_RATE>
          Bias rate [default: 0.0005]
      --variation-rate <VARIATION_RATE>
          Variation rate [default: 0.001]
  -h, --help
          Print help
  -V, --version

Basic example

Simple example: Create 1000 DNA sequences with 10000 nucleotides each, using default settings for mutation, bias, and variation rate in seq_generatoRS.

seq_generator --records-number 1000 --records-length 10000

To adjust mutation, bias, or variation rate, ensure values greater than 0 are used, as these parameters represent the maximum value when multiplied by the sequence length in seq_generatoRS.

Three files will be generated:

• mutation_x.txt: includes information about mutations and their locations.
• reference_x.fasta: stores the reference sequence, serving as the basis for mutation insertions.
• sequences_x.fasta: encompasses the specified number of sequences (--records-number) with mutations, variations, and bias.

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.

License

MIT