15 releases
0.2.0 | Aug 27, 2024 |
---|---|
0.1.14 | Aug 20, 2024 |
0.1.10 | Jul 25, 2024 |
#70 in Biology
723 downloads per month
3MB
9K
SLoC
grumpy
Re-implementation of gumpy in Rust for speed
Installation
Rust crate
cargo add grumpy
Python package
pip install bio-grumpy
Tests
Running Rust unit tests
cargo test
Coverage
Test coverage can be found with the use of tarpaulin
.
# Install tarpaulin on first run
cargo install cargo-tarpaulin
# Generate an HTML coverage report
cargo tarpaulin --no-dead-code --engine llvm --out html
lib.rs
:
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
Dependencies
~6–13MB
~151K SLoC