hashrope-bio

Computational biology applications of hashrope — O(log w) substring hashing for gene-level change detection, drug resistance screening, genomic region comparison, and tandem repeat analysis.

Features

• Gene-level change detection: Screen hundreds of genes between two genomes in O(G · log w) total time
• Drug resistance panels: Check N known mutation sites in O(N · log w) via codon hash comparison
• Pre-defined HIV-1 RT panels: 23 NNRTI + NRTI resistance sites from Stanford HIVDB
• Gene annotation loading: Parse UCSC refGene TSV for biologically meaningful queries

Quick start

Gene-level change detection

use hashrope::Arena;
use hashrope_bio::gene_diff::*;

// Load gene annotations
let genes = load_gene_regions("chr22_genes.tsv").unwrap();

// Build ropes for reference and sample genomes
let mut arena = Arena::new();
let ref_rope = arena.from_bytes(&ref_seq);
let sample_rope = arena.from_bytes(&sample_seq);

// Screen all genes — O(G · log w) total
let changed = screen_genes_single_arena(
    &mut arena, ref_rope, sample_rope, &genes, None,
);
println!("{} genes differ", changed.len());

// Detailed diff with exon-level resolution
let report = diff_genes_single_arena(
    &mut arena, ref_rope, sample_rope, &genes, None, true,
);
println!("{}", report.summary());
// Gene diff: 12/643 genes changed, 47/5127 exons changed
//   LARGE1 (650,315 bp): body changed, 3/14 exons differ

Drug resistance panels

use hashrope::Arena;
use hashrope_bio::resistance::*;
use hashrope_bio::gene::{make_synthetic_gene, mutate_codon};

let ref_gene = make_synthetic_gene(1680);
let mut sample = ref_gene.clone();
mutate_codon(&mut sample, 103); // K103N resistance mutation

let mut arena = Arena::new();
let ref_rope = arena.from_bytes(&ref_gene);
let sample_rope = arena.from_bytes(&sample);

let panel: Vec<_> = HIV_RT_NNRTI_PANEL.iter()
    .chain(HIV_RT_NRTI_PANEL.iter())
    .cloned().collect();

let results = check_panel_single_arena(&mut arena, ref_rope, sample_rope, &panel);
let mutant_sites: Vec<_> = results.iter()
    .filter(|r| r.is_mutant)
    .map(|r| r.position)
    .collect();
assert!(mutant_sites.contains(&103));

Validated results

All benchmarks use real biological data, not synthetic:

Benchmarks

Criterion benchmarks included:

cargo bench

License

MIT