biojs-io-fasta

npm install biojs-io-fasta

Use in your browser

<script src="http://wzrd.in/bundle/biojs-io-fasta@latest"></script>

• You can find a JSBin to play around with it.
• Remember that you need CORS to download files from other servers on the web

Methods

var Fasta = require('biojs-io-fasta');

read(url)

Parses an url an calls your parse method with the returned body.

Fasta.read("https://raw.githubusercontent.com/biojs-io/biojs-io-fasta/master/test/foo.fasta", function(err, model) {
	// model is the parsed url
});

If callback is undefined, read returns a promise.

var p = Fasta.read("https://raw.githubusercontent.com/biojs-io/biojs-io-fasta/master/test/foo.fasta");
// ...
p.then(function(model) {
	// model is the parsed url
}, function(err){
	console.error("err happened during downloading", err);
});

parse(str)

var seqs = Fasta.parse(str);

export(model)

var text = Fasta.export(seqs);

extend(customParser)

Thanks to @sillitoe you can provide a custom parser if your FASTA header is formatted "in weird and wonderful ways".

var customGetMeta = function(header) {
	return {
      id: "id",
      name: "name",
      // optional
      details: {
		foo: "bar"
      },
      // optional
      ids: {
		customId: "bar"
      }
    };
}
var altFasta = Fasta.extend(customGetMeta);

Take a look at tests for a better example of such a parser;

Sequence object

{
  seq: "ABC",
  name: "awesome seq",
  id: "unique id"
}

Develop

Install dependencies and execute the tests:

npm install
npm script compile && npm test

To build a JS file for the browser, execute:

npm run build-browser

License

Apache 2