phyloxml.js
phyloxml.js is a JavaScript program for reading (SAX style parser) and writing phylogenetic trees in phyloXML format.
phyloXML website: http://www.phyloxml.org/
Availability
Dependencies
- sax.js (1.2.4): https://www.npmjs.com/package/sax/v/1.2.4
Example
This basic example shows how to parse a phyloXML formatted String into to a object representing a phylogenetic tree. Followed by printing some elements and then converting the object back to a phyloXML formatted String.
Change './phyloxml' to 'phyloxml' if you use this code outside of this package
var phyloXml = require('./phyloxml').phyloXml;
phlyoXmlFormattedString = '<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' +
'xmlns="http://www.phyloxml.org" ' +
'xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd">' +
'<phylogeny rooted="true" rerootable="false">' +
'<clade><branch_length>0.2</branch_length>' +
'<clade><branch_length>0.4</branch_length><name>A</name></clade>' +
'<clade><branch_length>0.6</branch_length><name>B</name></clade>' +
'</clade>' +
'</phylogeny>' +
'</phyloxml>';
var phylogeneticTree = phyloXml.parse(phlyoXmlFormattedString, {trim: true, normalize: true})[0];
console.log('Root branch length : ' + phylogeneticTree.children[0].branch_length);
console.log('Node A name : ' + phylogeneticTree.children[0].children[0].name);
console.log('Node A branch length: ' + phylogeneticTree.children[0].children[0].branch_length);
console.log('Node B name : ' + phylogeneticTree.children[0].children[1].name);
console.log('Node B branch length: ' + phylogeneticTree.children[0].children[1].branch_length);
console.log('Entire tree in phyloXML format:');
console.log(phyloXml.toPhyloXML(phylogeneticTree, 4));
The output should be:
Root branch length : 0.2
Node A name : A
Node A branch length: 0.4
Node B name : B
Node B branch length: 0.6
Entire tree in phyloXML format:
<?xml version="1.0" encoding="UTF-8"?>
<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.20/phyloxml.xsd" xmlns="http://www.phyloxml.org">
<phylogeny rooted="true" rerootable="false">
<clade>
<branch_length>0.2</branch_length>
<clade>
<name>A</name>
<branch_length>0.4</branch_length>
</clade>
<clade>
<name>B</name>
<branch_length>0.6</branch_length>
</clade>
</clade>
</phylogeny>
</phyloxml>
Synchronous parsing of phyloXML-formatted String
var px = require('./phyloxml').phyloXml;
var phys = px.parse(phyloxmlText, {trim: true, normalize: true});
console.log(px.toPhyloXML(phys[0], 6));
Asynchronous parsing of phyloXML-formatted Stream
var fs = require('fs');
var px = require('./phyloxml').phyloXml;
var stream = fs.createReadStream(xmlFile, {encoding: 'utf8'});
px.parseAsync(stream, {trim: true, normalize: true});