Birdie

GitHub

birdie is a Deno module for bioinformatical analysis with the aim of evolving existing JavaScript code to WebAssembly-powered variants with improved computational performance. At the moment the project is in very early stages of development and all features are considered unstable and experimental.

Installation

birdie provides modules that can be imported into a JavaScript or Typescript application with a URL:

import * as pm from "https://deno.land/x/birdie/pattern_matching/mod.ts";

The WebAssembly needs to be initialized before use with the initWasm method:

await pm.initWasm();

As of right now, WebAssembly files are not locally cached along with JS/TS files in Deno, so you must pass --allow-net=deno.land in order to successfully run birdie.

Features

String Edit Distance

import * as distance from "https://deno.land/x/birdie/distance/mod.ts";

await distance.initWasm();

const x = "GTCTGCATGCG";
const y = "TTTAGCTAGCG";

// Hamming distance
const hammingDistance = distance.hamming(x, y);
console.log(hammingDistance); // 5n (BigInt)

// Levenshtein distance (Wagner-Fischer Algorithm)
const levenshteinDistance = distance.levenshtein(x, y);
console.log(levenshteinDistance);

// Myers' Algorithm
const myersDistance = distance.myers(x, y);
console.log(myersDistance);

Sequence Analysis

import * as sequence from "https://deno.land/x/birdie/sequence/mod.ts";

await sequence.initWasm();

const gcRatio = sequence.gcContent("GATATACA");
console.log(gcRatio); // 0.25

const gc3Ratio = sequence.gc3Content("GATATACA");
console.log(gc3Ratio); // 0.67

Pattern Matching

shift_and

import * as pm from "https://deno.land/x/birdie/pattern_matching/mod.ts";

await pm.initWasm();

const pattern = "AAAA";
const text = "ACGGCTAGAAAAGGCTAG";

const startPos = pm.shiftAnd(pattern, text);
console.log(startPos); // 8

Contributing

Any contributions are welcome and much appreciated!