hashrope-bio

Computational biology applications of hashrope — O(log w) substring hashing for genomic region comparison, mutation localization, tandem repeat compression, MD trajectory indexing, and drug resistance screening.

Install

pip install -e ".[genomics,bench,dev]"

Project structure

src/hashrope_bio/
├── genomics/          # FASTA loading, region queries, mutation search, tandem repeats
├── proteomics/        # MD trajectory frame comparison, periodic detection
└── cheminformatics/   # SMILES/InChI compound lookup, resistance panels
benchmarks/            # Experiment scripts (E-G1 through E-CG1)
scripts/               # Dataset download helpers
data/                  # Downloaded datasets (gitignored)
tests/                 # Unit tests

Experiments

See ../../experiments/EXPERIMENTS.md for the full protocol.

Run a benchmark:

python benchmarks/bench_region_query.py

Depends on

• hashrope (PyPI) — core data structure
• pysam / biopython — FASTA I/O
• MDAnalysis — trajectory I/O
• RDKit — cheminformatics

License

MIT