anarcism

anarcism is an independent reimplementation of ANARCI by James Dunbar and Charlotte M. Deane. It recognizes and IMGT-numbers antibody and T-cell-receptor variable domains. The engine is written in Rust and ships as a self-contained Python extension and WebAssembly package: analysis runs locally, with no HMMER binary, model download, or backend request.

It supports H/K/L/A/B/G/D chains, multidomain inputs, FASTA, configurable profile filters, alternative hits, V/J germline assignment, and VH/VL pair validation.

Features

Compared with the official ANARCI implementation:

• Self-contained installation without legacy hooks or HMMER
• Bounded-memory FASTA streaming with lower end-to-end time on large inputs
• Efficient multicore scaling
• WebAssembly package for browsers and Node.js

Python and CLI

pip install anarcism

import anarcism

result = anarcism.number_sequence(vh, assign_germline=True)
batch = anarcism.number_sequences(
    [("heavy", vh), ("light", vl)],
    workers=4,
)

# Iterable input and output keep large datasets bounded in memory.
with open("sequences.fasta") as fasta:
    for result in anarcism.iter_number_fasta(fasta, workers=4):
        consume(result)

The anarcism command and python -m anarcism provide ANARCI-compatible IMGT vertical, CSV, and hit-table output:

anarcism -i sequences.fasta -o numbered.anarci -p 8
anarcism -i sequences.fasta -o numbered --csv --assign_germline
anarcism -i sequences.fasta -o numbered.anarci -ht hits.txt
gunzip -c sequences.fasta.gz | anarcism -i - -o numbered.anarci

Run anarcism --help for the supported ANARCI flags. Only IMGT numbering is implemented; --hmmerpath is unnecessary because the backend is embedded.

anarcism is a drop-in replacement for the official ANARCI executable. To avoid changing scripts that call ANARCI, create a symlink:

ln -s "$(command -v anarcism)" "$(dirname "$(command -v anarcism)")/ANARCI"

JavaScript

npm install @revanta/anarcism

The package runs in modern browsers and Node.js 20.16+. It requires WebAssembly SIMD128 but not WASM threads or shared memory.

import { Anarcism } from "@revanta/anarcism";

const anarcism = await Anarcism.create();

const result = anarcism.numberSequence(vh, {
	allowedChains: ["H", "K", "L"],
	minBitScore: 80,
	alternativeHitCount: 3,
	assignGermline: true,
});

const batch = anarcism.numberSequences([
	{ id: "heavy", sequence: vh },
	{ id: "light", sequence: vl },
]);

const fastaResults = anarcism.numberFasta(`>heavy\n${vh}\n`);
const pair = anarcism.validateAntibodyPair(vh, vl);

Anarcism.create() loads the bundled anarcism.wasm; pass { source } with a URL, Response, bytes, or a compiled WebAssembly.Module to load it from elsewhere. Anarcism.createSync(bytesOrModule) instantiates without awaiting. Each instance owns an independent WebAssembly engine.

The synchronous API is suitable for interactive calls. For large batches in the browser, the worker-pool entry point runs independent WASM engines in Web Workers without blocking the page:

import { AnarcismWorkerPool } from "@revanta/anarcism/worker-pool";

const pool = await AnarcismWorkerPool.create({ workers: 4 });
const results = await pool.numberSequences(inputs);
pool.terminate();

Every asynchronous call accepts an AbortSignal. An aborted call rejects with signal.reason; the pool replaces the workers still computing it, so it stays usable at the same size:

const controller = new AbortController();
const pending = pool.numberSequences(inputs, { signal: controller.signal });
controller.abort();

const anarcism = await Anarcism.create({ signal: AbortSignal.timeout(5_000) });

TypeScript declarations are included. Invalid input raises AnarcismError with a stable code, message, and optional input ID.

Compatibility and size

The reference is ANARCI (OPIG) with HMMER 3.4, pinned in assets/MANIFEST.toml. The parity corpus holds 1,397 sequences (1,398 domains). It combines natural antibody and TCR sequences, IMGT germlines, and published PDB chains with deliberately adversarial stress tests: synthetic CDR-length ladders, framework indels, truncations, scFvs, multidomain constructs, constant domains, and non-antibody decoys.

A domain counts as exactly numbered only if every residue's IMGT position and insertion code, and its padded IMGT alignment, match ANARCI. Bit scores stay within 0.15 bits of HMMER's (mean 0.03) and E-values within 7% (mean 1.2%). The reference values live in tests/golden/corpus_reference.jsonl. The Rust and Python golden tests check every row against it, and npm --workspace packages/anarcism run parity reports domain, residue, and score parity for the WebAssembly build.

Development

The build needs Rust and Node.js 20.16+. rust-toolchain.toml pins the Rust release and installs the wasm32-unknown-unknown target. Install Binaryen for wasm-opt; without it the build ships the larger, unoptimized module and prints a warning. Python and ANARCI are only needed to regenerate the reference data; they are not runtime dependencies.

cargo test --workspace
cargo fmt --all --check
cargo clippy --workspace --all-targets -- -D warnings

npm ci
npm --workspace packages/anarcism run build
npm --workspace packages/anarcism test
npm --workspace packages/anarcism run test:browser
npm --workspace packages/anarcism run parity
npm --workspace demo run dev

The package build compiles anarcism-wasm for wasm32-unknown-unknown, optimizes it with wasm-opt -Oz, copies the JavaScript entry points, declarations, and license files next to it in packages/anarcism/dist/, and prints the size report.

Attribution and citation

anarcism reproduces the methods and data of the projects below. If you use it in published work, please cite them.

• ANARCI (Oxford Protein Informatics Group) defines the recognition, receptor classification, and numbering that anarcism reimplements. anarcism is validated against oxpig/ANARCI at commit 79f6c575056dedef86cb8f405ebb039197923eec, and its embedded profile HMMs and germline tables are generated with ANARCI's own build pipeline.

  Dunbar J, Deane CM. ANARCI: antigen receptor numbering and receptor classification. Bioinformatics 32(2):298–300 (2016). doi:10.1093/bioinformatics/btv552

• HMMER 3.4 (Sean R. Eddy and the HMMER developers) provides the profile-HMM search and scoring that ANARCI relies on. anarcism reimplements the parts ANARCI uses and is validated against HMMER 3.4.

  Eddy SR. Accelerated profile HMM searches. PLoS Computational Biology 7(10):e1002195 (2011). doi:10.1371/journal.pcbi.1002195

• IMGT®, the international ImMunoGeneTics information system® (Marie-Paule Lefranc and colleagues), defines the IMGT numbering scheme and supplies the germline sequences, from IMGT/GENE-DB release 202638-7.

  Lefranc M-P, Pommié C, Ruiz M, Giudicelli V, Foulquier E, Truong L, Thouvenin-Contet V, Lefranc G. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Developmental & Comparative Immunology 27(1):55–77 (2003). doi:10.1016/S0145-305X(02)00039-3

  Giudicelli V, Chaume D, Lefranc M-P. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Research 33:D256–D261 (2005). doi:10.1093/nar/gki010

License

The project's own code is licensed under the Apache License 2.0; see LICENSE. Third-party attributions and license texts are in THIRD_PARTY_NOTICES.md.