iham-parsers/test/test_issue3_iham.js

orthoxml, phyloxml and newick parsers for the iHam widget

var hogvis = require("../index.js");
var chai = require('chai'), assert = chai.assert, expect = chai.expect;
var fs = require('fs');
var parse_orthoxml = hogvis.parse_orthoxml, parse_newick = hogvis.parse_newick;

var sptree = '(Mus musculus,Homo sapiens)Root';
var orthoxml = '<orthoXML version="0.3">' +
        '<species name="Homo sapiens" NCBITaxId="9606">' +
        '<database name="someDB" version="42">' +
        '<genes>' +
        '<gene id="1" geneId="hsa1" protId="hsa1" />' +
        '</genes>' +
        '</database>' +
        '</species>' +
        '<species name="Mus musculus" NCBITaxId="10090">' +
        '<database name="someDB" version="42">' +
        '<genes>' +
        '<gene id="2" geneId="mmu1"/>' +
        '</genes>' +
        '</database>' +
        '</species>' +
        '<groups>' +
        '<orthologGroup>' +
        '<geneRef id="1" />' +
        '<geneRef id="2" />' +
        '</orthologGroup>' +
        '</groups>' +
        '</orthoXML>';

describe('Issue3 bug', function () {
    describe('issue3 example', function () {
        it('check per_species result', function () {
            var ex_per_spec = {
                "Mus musculus": {
                    "Mus musculus": [[2]],
                    Root: [[2]]},
                "Homo sapiens": {
                    "Homo sapiens": [[1]],
                    Root: [[1]]}
            };
            var data = parse_orthoxml(sptree, orthoxml);
            expect(ex_per_spec).to.eql(data.per_species);

        });
    });
});