Crate grumpy

Grumpy, genetic analysis in Rust.

This library provides a set of tools for genetic analysis, including:

• Genome representation
• Gene representation
• VCF file parsing
• Finding effects of a given VCF file at both genome and gene levels

Example

use grumpy::genome::{Genome, mutate};
use grumpy::vcf::VCFFile;
use grumpy::difference::{GenomeDifference, GeneDifference};
use grumpy::common::MinorType;

let mut reference = Genome::new("reference/MN908947.3.gb");
let vcf = VCFFile::new("test/dummy.vcf".to_string(), false, 3);
let mut sample = mutate(&reference, vcf);

let genome_diff = GenomeDifference::new(reference.clone(), sample.clone(), MinorType::COV);
for variant in genome_diff.variants.iter(){
   println!("{}", variant.variant);
}

for gene_name in sample.genes_with_mutations.clone().iter(){
  let gene_diff = GeneDifference::new(reference.get_gene(gene_name.clone()), sample.get_gene(gene_name.clone()), MinorType::COV);
  for mutation in gene_diff.mutations.iter(){
    println!("{}", mutation.mutation);
  }
}

Also provides an interface to this library as a Python module using PyO3. pip install bio-grumpy

Modules

common

Module of common structs and enums used throughout the program

difference

Module for handling differences between genomes and genes

gene

Module for handling gene data

genome

Module for handling genome data

vcf

Module for handling VCF files