Birdie - Bioinformatics for Deno

Birdie is a Deno project that provides users with fast WebAssembly code to run common tasks in bioinformatics on the Web, such as DNA sequence analysis. Birdie uses Rust in the background and makes use of its excellent bio crate, and aims to provide a straightforward API in Deno as well as high speed computation.

All of Birdie’s WebAssembly modules are benchmarked and compared with known JavaScript implementations where possible, as to deliver performant code that can be easily integrated with other Web technologies to develop a variety of bioinformatics applications.

Contents

1. Installation
2. Initializing the WebAssembly
3. Modules
   • distance
   • io
   • pattern_matching
   • sequence
4. Benchmarks

Installation

Birdie is an ES Module that can be imported into any Deno project. There is a TypeScript entrypoint named mod.ts for each of the different WebAssembly modules. For example, to load the pattern_matching module you would import the URL "https://deno.land/x/birdie/pattern_matching/mod.ts" into Deno:

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

For production use, pinpointing a version is recommended: "https://deno.land/x/birdie@v0.6.0/pattern_matching/mod.ts";

Importing specific components from a module is also possible, but you must always import the WebAssembly initialization function initWasm from the module:

import {
  initWasm,
  shiftAnd,
} from "https://deno.land/x/birdie/pattern_matching/mod.ts";

Initializing the WebAssembly

Birdie makes use of WebAssembly (WASM) modules. To load and instantiate these modules an initialization function needs to be called, which is exported as initWasm by default. It returns a Promise, so it needs to be awaited:

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

await patternMatching.initWasm();

After initialization, you can start using any of the exported WASM functions from Deno:

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

await patternMatching.initWasm();

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

const pos = patternMatching.shiftAnd(pattern, text);

At the moment of writing, Deno does not cache WASM modules locally along with JS/TS modules when deno cache or deno run is called. This means that Birdie’s WASM modules are currently fetched from their location on the Web, which requires you to allow net access to e.g. deno.land:

deno run --allow-net=deno.land mod.ts

If you want to use multiple birdie modules in a single file, you just have to create an alias for at least one of the imported init functions, though for clarity it is recommended to alias all in these kinds of scenarios:

import {
  initWasm as initPatternMatching,
  shiftAnd,
} from "https://deno.land/x/birdie/pattern_matching/mod.ts";
import {
  initWasm as initDistance,
  myers,
} from "https://deno.land/x/birdie/distance/mod.ts";

await initPatternMatching();
await initDistance();

Modules

TBD

distance

Calculate Levenshtein edit distance using one of several algorithms, including Wagner-Fischer and Myers’ Algorithm.

TBD

io

Read a FASTA file from stdin:

import * as io from "./io/mod.ts";
import { readAll } from "https://deno.land/std/streams/conversion.ts";

await io.initWasm();

io.readFastaFile(await readAll(Deno.stdin));

The readFastaFile function returns an array of objects with the following data:

{
  id:
  string;
  seq:
  string;
  len:
  number;
  desc:
  string;
}

pattern_matching

TBD

sequence

Perform DNA sequence analysis, such as calculating Guanine-Cytosine ratio.

TBD