iham-parsers/test/test_sample_orthoxml.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 = "(YEAST,(XENTR,((CANFA, WOLF),((MOUSE,RATNO)Rodents,(HUMAN,GORGO,PANTR)Primates)Euarchontoglires)Mammalia)Vertebrata)Eukaryota";

describe('SimpleEx OrthoXML', function () {
    describe('xrefs of genes', function () {
        it('resulting datastructure should contain xrefs corresponding to protId', function () {
            var xml = fs.readFileSync("./test/simpleEx.orthoxml");
            var data = parse_orthoxml(sptree, xml);

            var ex_xrefs = { '3': 'HUMAN3', '13': 'PANTR3', '14': 'PANTR4','23': 'CANFA3',
                '33': 'MOUSE3', '34': 'MOUSE4', '43': 'RATNO3', '53': 'XENTR3' };
            expect(ex_xrefs).to.eql(data.xrefs);
        });
    });

    describe('extracted species tree', function () {
        it('resulting species tree should be the trimed version of the input tree', function () {
            var xml = fs.readFileSync("./test/simpleEx.orthoxml");
            var data = parse_orthoxml(sptree, xml);
            var ex_tree = parse_newick.parse("(XENTR,(CANFA,((HUMAN,PANTR)Primates,(MOUSE,RATNO)Rodents)Euarchontoglires)Mammalia)Vertebrata;");
            expect(ex_tree).to.eql(data.tree);
        });
    });

    describe('per_species results', function(){
        it('resulting datastructure has right data', function(){
            var xml = fs.readFileSync("./test/simpleEx.orthoxml");
            var data = parse_orthoxml(sptree, xml);
            var ex_per_spec = { HUMAN: {
                HUMAN: [[3]],
                Primates: [[3],[]],
                Euarchontoglires: [[3],[]],
                Mammalia: [[3]],
                Vertebrata: [[3]] },
                PANTR:{
                    PANTR: [[13],[14]],
                    Primates: [[13],[14]],
                    Euarchontoglires: [[13],[14]],
                    Mammalia: [[13,14]],
                    Vertebrata: [[13,14]] },
                MOUSE:{
                    MOUSE: [[33],[34]],
                    Rodents: [[33],[34]],
                    Euarchontoglires: [[33],[34]],
                    Mammalia: [[33,34]],
                    Vertebrata: [[33,34]] },
                RATNO:{
                    RATNO: [[43]],
                    Rodents: [[43],[]],
                    Euarchontoglires: [[43],[]],
                    Mammalia: [[43]],
                    Vertebrata: [[43]]
                },
                CANFA: {
                    CANFA: [[23]],
                    Mammalia: [[23]],
                    Vertebrata: [[23]] },
                XENTR: {
                    XENTR: [[53]],
                    Vertebrata: [[53]] }
            };
            expect(ex_per_spec).to.eql(data.per_species);
        })
    })
});

describe('tnt newick parser', function () {
    describe('test functionality of tnt newick parser', function () {
        it('can parse a simple tree with internal labels', function() {
            var tree = parse_newick.parse("(A,B)C;");
            assert(tree.name, "C");
            assert(tree.children, [{name: "A"}, {name: "B"}]);
        });
        it("multifurcating tree", function(){
            var tree = parse_newick.parse("(A,B,C);");
            assert(3, tree.children.length);
        });
        it("quoted labels", function(){
            var tree = parse_newick.parse('(A,"species 1")"root";');
            assert("root", tree.name);
            assert("species 1", tree.children[1]);
        });
        it("labels can contain special chars if quoted", function(){
            var tree = parse_newick.parse('("A (strain B)", "B (stain ;)")"root & end";');
            assert("root & end", tree.name);
            assert("A (strain B)", tree.children[0]);
            assert("B (strain ;)", tree.children[1]);
        });
        it("nested levels of quotes", function(){
            var tree = parse_newick.parse('(("A","B somethin")"D /level", ("Q","R","S (strain A)")"TTT bla")"root";');
            let exp_tree = {name:"root", children:[
                {children:[{name:"A"},{name:"B somethin"}], name:"D /level"},
                {children:[{name:"Q"},{name:"R"},{name:"S (strain A)"}], name:"TTT bla"}
            ]};
            expect(exp_tree).eql(tree);
        })
    });
});