biojs-io-newick/test.js

Parses newick strings into JSON and JSON into newick

require('mocha');
var should = require('should');
var assert = require('chai').assert;


describe('BioJS2 Tree Test', function () {

	var parser = require('./src/newick');

	console.log(parser);
    var newick = "((human,chimp),mouse);";
    var tree = parser.parse_newick(newick);
		var backToNewick = parser.parse_json(tree);

    // Newick
    describe ('Newick reader', function () {
			it ("Exists and is called tree.parse_newick", function () {
			    assert.isDefined(parser.parse_newick);
			});

			it ("Can read a simple tree", function () {
			    assert.isDefined(tree);
			});
			it ("The returned tree has the correct structure", function () {
			    assert.property(tree, "name");
			    assert.property(tree, "children");
			    assert.property(tree.children[0], "name");
			    assert.property(tree.children[0], "children");
			    assert.strictEqual(tree.children[0].children[0].name, "human");
			    assert.notProperty(tree.children[0].children[0], "children");
			});

			it ("Reads the branch lenghts", function () {
			    var newick = "((human:0.2,chimp:0.3),mouse:0.5);";
			    var tree = parser.parse_newick(newick);
			    assert.closeTo(tree.children[1].branch_length, 0.5, 0.05);
			    assert.closeTo(tree.children[0].children[0].branch_length, 0.2, 0.05);
			    assert.closeTo(tree.children[0].children[1].branch_length, 0.3, 0.05);
			});
    });

		//JSON
		describe ('JSON reader', function () {
			it ("Exists and is called parser.parse_json", function () {
					assert.isDefined(parser.parse_json);
			});

			it ("Can read a simple JSON tree", function () {
					assert.isDefined(backToNewick);
			});
			it ("The returned tree has the correct structure", function () {
					assert.strictEqual(backToNewick, newick);
			});
		});

});