grumpy 1.1.4

Genetic analysis in Rust.
Documentation 
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//! 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`
use pyo3::prelude::*;

pub mod common;
pub mod difference;
pub mod gene;
pub mod genome;
pub mod vcf;

#[cfg(not(tarpaulin_include))]
#[pymodule]
/// 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
fn grumpy(m: &Bound<'_, PyModule>) -> PyResult<()> {
    m.add_class::<common::AltType>()?;
    m.add_class::<common::MinorType>()?;
    m.add_class::<common::VCFRow>()?;
    m.add_class::<common::Evidence>()?;

    m.add_class::<genome::Genome>()?;

    m.add_class::<gene::Gene>()?;

    m.add_class::<vcf::VCFFile>()?;

    m.add_class::<difference::GenomeDifference>()?;
    m.add_class::<difference::GeneDifference>()?;

    m.add_function(wrap_pyfunction!(genome::mutate, m)?)?;
    m.add_function(wrap_pyfunction!(common::thread_setup, m)?)?;
    m.add("__version__", env!("CARGO_PKG_VERSION"))?;

    Ok(())
}